diff --git a/main/404.html b/main/404.html
index 2b73d161..ac154217 100644
--- a/main/404.html
+++ b/main/404.html
@@ -6,22 +6,13 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <title>Page not found (404) • hermes</title>
-<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="https://insightsengineering.github.io/hermes/favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="https://insightsengineering.github.io/hermes/favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="https://insightsengineering.github.io/hermes/apple-touch-icon.png">
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="https://insightsengineering.github.io/hermes/apple-touch-icon-120x120.png">
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="https://insightsengineering.github.io/hermes/apple-touch-icon-76x76.png">
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="https://insightsengineering.github.io/hermes/apple-touch-icon-60x60.png">
 <script src="https://insightsengineering.github.io/hermes/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="https://insightsengineering.github.io/hermes/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="https://insightsengineering.github.io/hermes/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://insightsengineering.github.io/hermes/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
+<script src="https://insightsengineering.github.io/hermes/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://insightsengineering.github.io/hermes/deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="https://insightsengineering.github.io/hermes/deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="https://insightsengineering.github.io/hermes/deps/headroom-0.11.0/headroom.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/search-1.0.0/fuse.min.js"></script><script src="https://insightsengineering.github.io/hermes/deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="https://insightsengineering.github.io/hermes/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 <meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script src="https://insightsengineering.github.io/hermes/NA">
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script src="https://insightsengineering.github.io/hermes/NA">
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -31,60 +22,37 @@
 </head>
 <body>
     <a href="https://insightsengineering.github.io/hermes/#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="https://insightsengineering.github.io/hermes/index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="https://insightsengineering.github.io/hermes/articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="https://insightsengineering.github.io/hermes/reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="https://insightsengineering.github.io/hermes/news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
+<li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/hermes/articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/hermes/reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/hermes/news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="https://insightsengineering.github.io/hermes/logo.png" class="logo" alt=""><h1>Page not found (404)</h1>
-      
+
     </div>
 
 Content not found. Please use links in the navbar.
@@ -98,15 +66,15 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index 0905866b..0d6cae3f 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contribution Guidelines • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contribution Guidelines"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contribution Guidelines • hermes</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contribution Guidelines"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,55 +7,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="logo.png" class="logo" alt=""><h1>Contribution Guidelines</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/.github/CONTRIBUTING.md" class="external-link"><code>.github/CONTRIBUTING.md</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/.github/CONTRIBUTING.md" class="external-link"><code>.github/CONTRIBUTING.md</code></a></small>
     </div>
 
 <div id="contribution-guidelines" class="section level1">
@@ -175,7 +150,7 @@ <h2 id="questions">Questions<a class="anchor" aria-label="anchor" href="#questio
 </div>
 </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -184,14 +159,14 @@ <h2 id="questions">Questions<a class="anchor" aria-label="anchor" href="#questio
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/apple-touch-icon-120x120.png b/main/apple-touch-icon-120x120.png
deleted file mode 100644
index e65aeb76..00000000
Binary files a/main/apple-touch-icon-120x120.png and /dev/null differ
diff --git a/main/apple-touch-icon-152x152.png b/main/apple-touch-icon-152x152.png
deleted file mode 100644
index b389254e..00000000
Binary files a/main/apple-touch-icon-152x152.png and /dev/null differ
diff --git a/main/apple-touch-icon-180x180.png b/main/apple-touch-icon-180x180.png
deleted file mode 100644
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diff --git a/main/articles/hermes.html b/main/articles/hermes.html
index 05e2ef88..59149d86 100644
--- a/main/articles/hermes.html
+++ b/main/articles/hermes.html
@@ -5,25 +5,13 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="hermes">
 <title>Introduction to `hermes` • hermes</title>
-<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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-<meta property="og:description" content="hermes">
-<meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to `hermes`">
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
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   gtag('js', new Date());
@@ -33,54 +21,31 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="active nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
+<li class="active nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -121,7 +86,7 @@ <h4 data-toc-skip class="author">Daniel Sabanés
       
                   
       
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/vignettes/hermes.Rmd" class="external-link"><code>vignettes/hermes.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/vignettes/hermes.Rmd" class="external-link"><code>vignettes/hermes.Rmd</code></a></small>
       <div class="d-none name"><code>hermes.Rmd</code></div>
     </div>
 
@@ -366,13 +331,12 @@ <h3 id="importing-a-matrix">Importing a Matrix<a class="anchor" aria-label="anch
 <span><span class="co">#&gt; additional gene information(3): GeneID SYMBOL chromosome_name</span></span>
 <span><span class="co">#&gt; samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R</span></span>
 <span><span class="co">#&gt;   06520019C0023R</span></span>
-<span><span class="co">#&gt; additional sample information(72): Filename SampleID ... TTYPE STDSSDY</span></span></code></pre></div>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">object3</span><span class="op">)</span></span>
+<span><span class="co">#&gt; additional sample information(72): Filename SampleID ... TTYPE STDSSDY</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">object3</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] TRUE</span></span></code></pre></div>
 <p>Note that we can easily access the counts assay (matrix) in the final
 object with <code><a href="../reference/counts.html">counts()</a></code>:</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">cnts</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/counts.html">counts</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span><span class="va">cnts</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span></span>
 <span><span class="co">#&gt;                  06520011B0023R 06520067C0018R 06520063C0043R</span></span>
@@ -398,12 +362,12 @@ <h3 id="connection-to-database">Connection to Database<a class="anchor" aria-lab
 <p>In order to save time during vignette build, we zoom in here on a
 subset of the original <code>object</code> containing only the first 10
 genes.</p>
-<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">small_object</span> <span class="op">&lt;-</span> <span class="va">object</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span>, <span class="op">]</span></span></code></pre></div>
 <p>The corresponding function takes the common gene ID prefix as
 argument to determine the format of the gene IDs and the filter variable
 to use in the query later on.</p>
-<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">httr</span><span class="fu">::</span><span class="fu"><a href="https://httr.r-lib.org/reference/set_config.html" class="external-link">set_config</a></span><span class="op">(</span><span class="fu">httr</span><span class="fu">::</span><span class="fu"><a href="https://httr.r-lib.org/reference/config.html" class="external-link">config</a></span><span class="op">(</span>ssl_verifypeer <span class="op">=</span> <span class="fl">0L</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="va">connection</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/connect_biomart.html">connect_biomart</a></span><span class="op">(</span><span class="fu"><a href="../reference/prefix.html">prefix</a></span><span class="op">(</span><span class="va">small_object</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>Here we are using the <code><a href="../reference/prefix.html">prefix()</a></code> method to access the
@@ -414,7 +378,7 @@ <h3 id="querying-and-saving-annotations">Querying and Saving Annotations<a class
 </h3>
 <p>Then the second step is to query the gene annotations and save them
 in the object.</p>
-<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/annotation.html">annotation</a></span><span class="op">(</span><span class="va">small_object</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/query.html">query</a></span><span class="op">(</span><span class="fu"><a href="../reference/genes.html">genes</a></span><span class="op">(</span><span class="va">small_object</span><span class="op">)</span>, <span class="va">connection</span><span class="op">)</span></span></code></pre></div>
 <p>Here we are using the <code><a href="../reference/genes.html">genes()</a></code> method to access the gene
 IDs (row names) of the <code>HermesData</code> object. Note that not all
@@ -440,11 +404,10 @@ <h3 id="automatic-gene-and-sample-flagging">Automatic Gene and Sample Flagging<a
 <p>Thresholds for the above flags can be initialized with
 <code><a href="../reference/control_quality.html">control_quality()</a></code>, and the flags are added with
 <code><a href="../reference/quality_flags.html">add_quality_flags()</a></code>.</p>
-<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">my_controls</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/control_quality.html">control_quality</a></span><span class="op">(</span>min_cpm <span class="op">=</span> <span class="fl">10</span>, min_cpm_prop <span class="op">=</span> <span class="fl">0.4</span>, min_corr <span class="op">=</span> <span class="fl">0.4</span>, min_depth <span class="op">=</span> <span class="fl">1e4</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Loading required namespace: testthat</span></span></code></pre></div>
-<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">object_flagged</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/quality_flags.html">add_quality_flags</a></span><span class="op">(</span><span class="va">object</span>, control <span class="op">=</span> <span class="va">my_controls</span><span class="op">)</span></span></code></pre></div>
+<span><span class="co">#&gt; Loading required namespace: testthat</span></span>
+<span><span class="va">object_flagged</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/quality_flags.html">add_quality_flags</a></span><span class="op">(</span><span class="va">object</span>, control <span class="op">=</span> <span class="va">my_controls</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="manual-sample-flagging">Manual Sample Flagging<a class="anchor" aria-label="anchor" href="#manual-sample-flagging"></a>
@@ -452,27 +415,25 @@ <h3 id="manual-sample-flagging">Manual Sample Flagging<a class="anchor" aria-lab
 <p>Sometimes it is necessary to manually flag certain samples as
 technical failures, e.g. after looking at one of the analyses discussed
 below. This is possible, too.</p>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">object_flagged</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/set_tech_failure.html">set_tech_failure</a></span><span class="op">(</span><span class="va">object_flagged</span>, sample_ids <span class="op">=</span> <span class="st">"06520011B0023R"</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="accessing-flags">Accessing Flags<a class="anchor" aria-label="anchor" href="#accessing-flags"></a>
 </h3>
 <p>All flags have access functions.</p>
-<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/quality_flags.html">get_tech_failure</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R </span></span>
 <span><span class="co">#&gt;           TRUE          FALSE          FALSE          FALSE          FALSE </span></span>
 <span><span class="co">#&gt; 06520103C0017R </span></span>
-<span><span class="co">#&gt;          FALSE</span></span></code></pre></div>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/quality_flags.html">get_low_depth</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="co">#&gt;          FALSE</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/quality_flags.html">get_low_depth</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R </span></span>
 <span><span class="co">#&gt;          FALSE          FALSE          FALSE          FALSE          FALSE </span></span>
 <span><span class="co">#&gt; 06520103C0017R </span></span>
-<span><span class="co">#&gt;          FALSE</span></span></code></pre></div>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/quality_flags.html">get_low_expression</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="co">#&gt;          FALSE</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/quality_flags.html">get_low_expression</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt;     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835 </span></span>
 <span><span class="co">#&gt;             TRUE            FALSE             TRUE             TRUE </span></span>
 <span><span class="co">#&gt; GeneID:102466731     GeneID:64881 </span></span>
@@ -490,7 +451,7 @@ <h3 id="based-on-default-qc-flags">Based on Default QC Flags<a class="anchor" ar
 <p>This is simple with the <code><a href="../reference/filter.html">filter()</a></code> function. It is also
 possible to selectively only filter the genes or the samples using the
 <code>what</code> argument.</p>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">object_flagged_filtered</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/filter.html">filter</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span></span>
 <span><span class="va">object_flagged_genes_filtered</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/filter.html">filter</a></span><span class="op">(</span><span class="va">object_flagged</span>, what <span class="op">=</span> <span class="st">"genes"</span><span class="op">)</span></span></code></pre></div>
 </div>
@@ -502,13 +463,12 @@ <h3 id="based-on-custom-variables">Based on Custom Variables<a class="anchor" ar
 the gene information variables, and samples can be filtered with the
 <code>select</code> argument using the sample information variables. In
 order to see which ones are available these can be queries first.</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "symbol"              "desc"                "GeneID"             </span></span>
 <span><span class="co">#&gt; [4] "chromosome"          "size"                "SYMBOL"             </span></span>
-<span><span class="co">#&gt; [7] "chromosome_name"     "low_expression_flag"</span></span></code></pre></div>
-<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [7] "chromosome_name"     "low_expression_flag"</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt;  [1] "Filename"          "SampleID"          "AGEGRP"           </span></span>
 <span><span class="co">#&gt;  [4] "AGE18"             "STDDRS"            "STDDRSD"          </span></span>
 <span><span class="co">#&gt;  [7] "STDSSDT"           "TRTDRS"            "TRTDRSD"          </span></span>
@@ -533,16 +493,13 @@ <h3 id="based-on-custom-variables">Based on Custom Variables<a class="anchor" ar
 <span><span class="co">#&gt; [64] "DISCSTUD"          "DISCDEAT"          "DISCAE"           </span></span>
 <span><span class="co">#&gt; [67] "DISTRTFL"          "AEWITHFL"          "ALIVDT"           </span></span>
 <span><span class="co">#&gt; [70] "COHORT"            "TTYPE"             "STDSSDY"          </span></span>
-<span><span class="co">#&gt; [73] "low_depth_flag"    "tech_failure_flag"</span></span></code></pre></div>
-<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">$</span><span class="va">chromosome</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [73] "low_depth_flag"    "tech_failure_flag"</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">)</span><span class="op">$</span><span class="va">chromosome</span><span class="op">)</span></span>
 <span><span class="co">#&gt; [1] "7"          "12"         "GL000220.1" "17"         "16"        </span></span>
-<span><span class="co">#&gt; [6] "13"</span></span></code></pre></div>
-<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">$</span><span class="va">ARMCD</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] "COH1"  "COH1"  "COH8"  "COH12" "COH9O" "COH9E"</span></span></code></pre></div>
-<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">object_flagged_subsetted</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/subset.html">subset</a></span><span class="op">(</span></span>
+<span><span class="co">#&gt; [6] "13"</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">object_flagged</span><span class="op">$</span><span class="va">ARMCD</span><span class="op">)</span></span>
+<span><span class="co">#&gt; [1] "COH1"  "COH1"  "COH8"  "COH12" "COH9O" "COH9E"</span></span>
+<span><span class="va">object_flagged_subsetted</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/subset.html">subset</a></span><span class="op">(</span></span>
 <span>  <span class="va">object_flagged</span>,</span>
 <span>  subset <span class="op">=</span> <span class="va">chromosome</span> <span class="op">==</span> <span class="st">"5"</span>,</span>
 <span>  select <span class="op">=</span> <span class="va">ARMCD</span> <span class="op">==</span> <span class="st">"COH1"</span></span>
@@ -558,25 +515,25 @@ <h2 id="normalizing-counts">Normalizing Counts<a class="anchor" aria-label="anch
 counts by the variance stabilizing transformation (<code>vst</code>) and
 the regularized log transformation (<code>rlog</code>) as proposed in
 the <code>DESeq2</code> package.</p>
-<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">object_normalized</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/normalize.html">normalize</a></span><span class="op">(</span><span class="va">object_flagged_filtered</span><span class="op">)</span></span>
 <span><span class="co">#&gt; -- note: fitType='parametric', but the dispersion trend was not well captured by the</span></span>
 <span><span class="co">#&gt;    function: y = a/x + b, and a local regression fit was automatically substituted.</span></span>
 <span><span class="co">#&gt;    specify fitType='local' or 'mean' to avoid this message next time.</span></span></code></pre></div>
-<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">object_rlog_normalized</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/normalize.html">normalize</a></span><span class="op">(</span><span class="va">object_flagged_filtered</span>, <span class="st">"rlog"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; -- note: fitType='parametric', but the dispersion trend was not well captured by the</span></span>
 <span><span class="co">#&gt;    function: y = a/x + b, and a local regression fit was automatically substituted.</span></span>
 <span><span class="co">#&gt;    specify fitType='local' or 'mean' to avoid this message next time.</span></span></code></pre></div>
 <p>The corresponding assays are saved in the object and can be accessed
 with <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">assay()</a></code>.</p>
-<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">assay</a></span><span class="op">(</span><span class="va">object_normalized</span>, <span class="st">"tpm"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span></span>
 <span><span class="co">#&gt;               06520067C0018R 06520063C0043R 06520105C0017R</span></span>
 <span><span class="co">#&gt; GeneID:10677        4.096418       3.323016       7.714990</span></span>
 <span><span class="co">#&gt; GeneID:286205       2.985506       3.182624       3.769962</span></span>
 <span><span class="co">#&gt; GeneID:8365        11.711741      12.421108      12.466491</span></span></code></pre></div>
-<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">assay</a></span><span class="op">(</span><span class="va">object_rlog_normalized</span>, <span class="st">"rlog"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span></span>
 <span><span class="co">#&gt;               06520067C0018R 06520063C0043R 06520105C0017R</span></span>
 <span><span class="co">#&gt; GeneID:10677        8.101651       7.153488      10.281393</span></span>
@@ -584,7 +541,7 @@ <h2 id="normalizing-counts">Normalizing Counts<a class="anchor" aria-label="anch
 <span><span class="co">#&gt; GeneID:8365        10.023097      10.163191       9.935722</span></span></code></pre></div>
 <p>The used control settings can be accessed afterwards from the
 metadata of the object:</p>
-<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/metadata.html">metadata</a></span><span class="op">(</span><span class="va">object_normalized</span><span class="op">)</span></span>
 <span><span class="co">#&gt; $control_quality_flags</span></span>
 <span><span class="co">#&gt; $control_quality_flags$min_cpm</span></span>
@@ -615,16 +572,15 @@ <h2 id="normalizing-counts">Normalizing Counts<a class="anchor" aria-label="anch
 <p>Note that also the filtering settings are saved in here. For custom
 normalization options, use <code><a href="../reference/control_normalize.html">control_normalize()</a></code>. For
 example, to not use log scale but the original scale of the counts:</p>
-<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">object_normalized_original</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/normalize.html">normalize</a></span><span class="op">(</span></span>
 <span>  <span class="va">object_flagged_filtered</span>,</span>
 <span>  control <span class="op">=</span> <span class="fu"><a href="../reference/control_normalize.html">control_normalize</a></span><span class="op">(</span>log <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span><span class="co">#&gt; -- note: fitType='parametric', but the dispersion trend was not well captured by the</span></span>
 <span><span class="co">#&gt;    function: y = a/x + b, and a local regression fit was automatically substituted.</span></span>
-<span><span class="co">#&gt;    specify fitType='local' or 'mean' to avoid this message next time.</span></span></code></pre></div>
-<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">assay</a></span><span class="op">(</span><span class="va">object_normalized_original</span>, <span class="st">"tpm"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span></span>
+<span><span class="co">#&gt;    specify fitType='local' or 'mean' to avoid this message next time.</span></span>
+<span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">assay</a></span><span class="op">(</span><span class="va">object_normalized_original</span>, <span class="st">"tpm"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span></span>
 <span><span class="co">#&gt;               06520067C0018R 06520063C0043R 06520105C0017R</span></span>
 <span><span class="co">#&gt; GeneID:10677       16.105854       9.007544       209.1084</span></span>
 <span><span class="co">#&gt; GeneID:286205       6.920033       8.079569        12.6418</span></span>
@@ -638,7 +594,7 @@ <h3 id="simple-plots">Simple Plots<a class="anchor" aria-label="anchor" href="#s
 </h3>
 <p>A series of simple descriptive plots can be obtained by just calling
 <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> on an object.</p>
-<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-30-1.png" width="700"><img src="hermes_files/figure-html/unnamed-chunk-30-2.png" width="700"><img src="hermes_files/figure-html/unnamed-chunk-30-3.png" width="700"><img src="hermes_files/figure-html/unnamed-chunk-30-4.png" width="700"><img src="hermes_files/figure-html/unnamed-chunk-30-5.png" width="700"></p>
 <p>Note that individual plots from these can be produced with the series
@@ -646,7 +602,7 @@ <h3 id="simple-plots">Simple Plots<a class="anchor" aria-label="anchor" href="#s
 detailed list. Then, these can be customized further. For example, we
 can change the number and color of the bins in the library size
 histogram:</p>
-<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/draw_libsize_hist.html">draw_libsize_hist</a></span><span class="op">(</span><span class="va">object</span>, bins <span class="op">=</span> <span class="fl">10L</span>, fill <span class="op">=</span> <span class="st">"blue"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-31-1.png" width="700"></p>
 </div>
@@ -654,13 +610,13 @@ <h3 id="simple-plots">Simple Plots<a class="anchor" aria-label="anchor" href="#s
 <h3 id="top-genes">Top Genes<a class="anchor" aria-label="anchor" href="#top-genes"></a>
 </h3>
 <p>Top genes can be calculated and visualized in a barplot.</p>
-<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">most_expr_genes</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/top_genes.html">top_genes</a></span><span class="op">(</span><span class="va">object_normalized</span>, assay_name <span class="op">=</span> <span class="st">"tpm"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">most_expr_genes</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-32-1.png" width="700"></p>
 <p>By passing another summary function, also the variability can be
 ranked for example.</p>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">most_var_genes</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/top_genes.html">top_genes</a></span><span class="op">(</span><span class="va">object_normalized</span>, summary_fun <span class="op">=</span> <span class="va">rowSds</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">most_var_genes</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-33-1.png" width="700"></p>
@@ -669,12 +625,12 @@ <h3 id="top-genes">Top Genes<a class="anchor" aria-label="anchor" href="#top-gen
 <h3 id="heatmap-of-genes-among-samples">Heatmap of Genes among Samples<a class="anchor" aria-label="anchor" href="#heatmap-of-genes-among-samples"></a>
 </h3>
 <p>Relative expression of genes can be displayed using a heatmap</p>
-<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/draw_heatmap.html">draw_heatmap</a></span><span class="op">(</span><span class="va">object</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">20</span><span class="op">]</span>, assay_name <span class="op">=</span> <span class="st">"counts"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-34-1.png" width="700"></p>
 <p>The heatmap can be grouped by labels in the <code>HermesData</code>
 object, such as <code>"COUNTRY"</code> or <code>"AGEGRP"</code>.</p>
-<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/draw_heatmap.html">draw_heatmap</a></span><span class="op">(</span><span class="va">object</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">20</span><span class="op">]</span>, assay_name <span class="op">=</span> <span class="st">"counts"</span>, col_data_annotation <span class="op">=</span> <span class="st">"COUNTRY"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-35-1.png" width="700"></p>
 </div>
@@ -685,7 +641,7 @@ <h3 id="correlation-between-samples">Correlation between Samples<a class="anchor
 <code><a href="../reference/correlate.html">correlate()</a></code> function. This can be visualized in a heatmap
 using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> again. See <code><a href="../reference/calc_cor.html">?calc_cor</a></code> for
 detailed options.</p>
-<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">cor_mat</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/correlate.html">correlate</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">cor_mat</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-36-1.png" width="700"></p>
@@ -700,7 +656,7 @@ <h3 id="pca-of-samples">PCA of Samples<a class="anchor" aria-label="anchor" href
 </h3>
 <p>PCA can be performed with <code><a href="../reference/calc_pca.html">calc_pca()</a></code>. The result can be
 summarized or plotted.</p>
-<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">pca_res</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/calc_pca.html">calc_pca</a></span><span class="op">(</span><span class="va">object_normalized</span>, assay_name <span class="op">=</span> <span class="st">"tpm"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_res</span><span class="op">)</span><span class="op">$</span><span class="va">importance</span></span>
 <span><span class="co">#&gt;                             PC1      PC2      PC3      PC4      PC5      PC6</span></span>
@@ -712,17 +668,16 @@ <h3 id="pca-of-samples">PCA of Samples<a class="anchor" aria-label="anchor" href
 <span><span class="co">#&gt; Proportion of Variance 0.047520 0.039550 0.035920 0.033160 0.030850 0.025700</span></span>
 <span><span class="co">#&gt; Cumulative Proportion  0.754200 0.793750 0.829670 0.862830 0.893680 0.919380</span></span>
 <span><span class="co">#&gt;                           PC13     PC14     PC15     PC16     PC17             </span></span>
-<span><span class="co">#&gt; Standard deviation     6.92755 6.532485 5.501383 5.151959 3.983283 2.272579e-14</span></span>
+<span><span class="co">#&gt; Standard deviation     6.92755 6.532485 5.501383 5.151959 3.983283 2.280611e-14</span></span>
 <span><span class="co">#&gt; Proportion of Variance 0.02369 0.021060 0.014940 0.013100 0.007830 0.000000e+00</span></span>
-<span><span class="co">#&gt; Cumulative Proportion  0.94307 0.964130 0.979070 0.992170 1.000000 1.000000e+00</span></span></code></pre></div>
-<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">pca_res</span><span class="op">)</span></span></code></pre></div>
+<span><span class="co">#&gt; Cumulative Proportion  0.94307 0.964130 0.979070 0.992170 1.000000 1.000000e+00</span></span>
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">pca_res</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-37-1.png" width="700"></p>
 <p>Note that various options are available for the plot, for example we
 can look at different principal components, and color the samples by
 sample variables. See <code><a href="https://rdrr.io/pkg/ggfortify/man/autoplot.pca_common.html" class="external-link">?ggfortify::autoplot.prcomp</a></code> for
 details.</p>
-<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span></span>
 <span>  <span class="va">pca_res</span>,</span>
 <span>  x <span class="op">=</span> <span class="fl">2</span>, y <span class="op">=</span> <span class="fl">3</span>,</span>
@@ -737,7 +692,7 @@ <h3 id="correlation-with-sample-variables">Correlation with Sample Variables<a c
 components with the sample variables. We obtain a matrix of R-squared
 (R2) values for all combinations, which can again be visualized as a
 heatmap. See <code><a href="../reference/pca_cor_samplevar.html">?pca_cor_samplevar</a></code> for details.</p>
-<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">pca_cor</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/correlate.html">correlate</a></span><span class="op">(</span><span class="va">pca_res</span>, <span class="va">object_normalized</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">pca_cor</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-39-1.png" width="700"></p>
@@ -773,7 +728,7 @@ <h2 id="differential-expression">Differential Expression<a class="anchor" aria-l
 filtered object (normalization of counts is not required) the variable
 name of the factor to contrast the samples needs to be provided to
 <code><a href="../reference/diff_expression.html">diff_expression()</a></code>.</p>
-<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/df_cols_to_factor.html">df_cols_to_factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="va">diff_res</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/diff_expression.html">diff_expression</a></span><span class="op">(</span><span class="va">object</span>, group <span class="op">=</span> <span class="st">"SEX"</span>, method <span class="op">=</span> <span class="st">"voom"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">diff_res</span><span class="op">)</span></span>
@@ -789,7 +744,7 @@ <h2 id="differential-expression">Differential Expression<a class="anchor" aria-l
 and logical variables to factor variables. This is one possible way here
 to ensure that the utilized group variable is a factor.</p>
 <p>Afterwards a standard volcano plot can be produced.</p>
-<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">diff_res</span>, log2_fc_thresh <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></span></code></pre></div>
 <p><img src="hermes_files/figure-html/unnamed-chunk-41-1.png" width="700"></p>
 </div>
@@ -808,10 +763,10 @@ <h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></
 <h2 class="unnumbered" id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h2>
 <p>Here is the output of <code><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo()</a></code> on the system on
-which this document was compiled running <code>pandoc</code> 3.2:</p>
-<pre><code><span><span class="co">#&gt; R version 4.4.0 (2024-04-24)</span></span>
+which this document was compiled running <code>pandoc</code> 3.4:</p>
+<pre><code><span><span class="co">#&gt; R version 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">#&gt; Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">#&gt; Running under: Ubuntu 22.04.4 LTS</span></span>
+<span><span class="co">#&gt; Running under: Ubuntu 22.04.5 LTS</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Matrix products: default</span></span>
 <span><span class="co">#&gt; BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
@@ -833,77 +788,76 @@ <h2 class="unnumbered" id="session-info">Session Info<a class="anchor" aria-labe
 <span><span class="co">#&gt; [8] base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt;  [1] hermes_1.7.2.9000           SummarizedExperiment_1.34.0</span></span>
-<span><span class="co">#&gt;  [3] Biobase_2.64.0              GenomicRanges_1.56.1       </span></span>
-<span><span class="co">#&gt;  [5] GenomeInfoDb_1.40.1         IRanges_2.38.0             </span></span>
-<span><span class="co">#&gt;  [7] S4Vectors_0.42.0            BiocGenerics_0.50.0        </span></span>
-<span><span class="co">#&gt;  [9] MatrixGenerics_1.16.0       matrixStats_1.3.0          </span></span>
+<span><span class="co">#&gt;  [1] hermes_1.7.2.9003           SummarizedExperiment_1.36.0</span></span>
+<span><span class="co">#&gt;  [3] Biobase_2.66.0              GenomicRanges_1.58.0       </span></span>
+<span><span class="co">#&gt;  [5] GenomeInfoDb_1.42.1         IRanges_2.40.1             </span></span>
+<span><span class="co">#&gt;  [7] S4Vectors_0.44.0            BiocGenerics_0.52.0        </span></span>
+<span><span class="co">#&gt;  [9] MatrixGenerics_1.18.0       matrixStats_1.4.1          </span></span>
 <span><span class="co">#&gt; [11] ggfortify_0.4.17            ggplot2_3.5.1              </span></span>
-<span><span class="co">#&gt; [13] BiocStyle_2.32.1           </span></span>
+<span><span class="co">#&gt; [13] BiocStyle_2.34.0           </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
-<span><span class="co">#&gt;   [1] Rdpack_2.6                  DBI_1.2.3                  </span></span>
-<span><span class="co">#&gt;   [3] httr2_1.0.1                 gridExtra_2.3              </span></span>
-<span><span class="co">#&gt;   [5] testthat_3.2.1.1            biomaRt_2.60.1             </span></span>
+<span><span class="co">#&gt;   [1] Rdpack_2.6.2                DBI_1.2.3                  </span></span>
+<span><span class="co">#&gt;   [3] httr2_1.0.7                 gridExtra_2.3              </span></span>
+<span><span class="co">#&gt;   [5] testthat_3.2.2              biomaRt_2.62.0             </span></span>
 <span><span class="co">#&gt;   [7] rlang_1.1.4                 magrittr_2.0.3             </span></span>
-<span><span class="co">#&gt;   [9] clue_0.3-65                 GetoptLong_1.0.5           </span></span>
-<span><span class="co">#&gt;  [11] compiler_4.4.0              RSQLite_2.3.7              </span></span>
+<span><span class="co">#&gt;   [9] clue_0.3-66                 GetoptLong_1.0.5           </span></span>
+<span><span class="co">#&gt;  [11] compiler_4.4.1              RSQLite_2.3.9              </span></span>
 <span><span class="co">#&gt;  [13] png_0.1-8                   systemfonts_1.1.0          </span></span>
 <span><span class="co">#&gt;  [15] vctrs_0.6.5                 stringr_1.5.1              </span></span>
 <span><span class="co">#&gt;  [17] pkgconfig_2.0.3             shape_1.4.6.1              </span></span>
 <span><span class="co">#&gt;  [19] crayon_1.5.3                fastmap_1.2.0              </span></span>
-<span><span class="co">#&gt;  [21] magick_2.8.3                dbplyr_2.5.0               </span></span>
-<span><span class="co">#&gt;  [23] backports_1.5.0             XVector_0.44.0             </span></span>
+<span><span class="co">#&gt;  [21] magick_2.8.5                dbplyr_2.5.0               </span></span>
+<span><span class="co">#&gt;  [23] backports_1.5.0             XVector_0.46.0             </span></span>
 <span><span class="co">#&gt;  [25] labeling_0.4.3              utf8_1.2.4                 </span></span>
-<span><span class="co">#&gt;  [27] rmarkdown_2.27              UCSC.utils_1.0.0           </span></span>
-<span><span class="co">#&gt;  [29] ragg_1.3.2                  purrr_1.0.2                </span></span>
-<span><span class="co">#&gt;  [31] bit_4.0.5                   xfun_0.45                  </span></span>
-<span><span class="co">#&gt;  [33] MultiAssayExperiment_1.30.2 zlibbioc_1.50.0            </span></span>
-<span><span class="co">#&gt;  [35] cachem_1.1.0                jsonlite_1.8.8             </span></span>
-<span><span class="co">#&gt;  [37] progress_1.2.3              EnvStats_2.8.1             </span></span>
-<span><span class="co">#&gt;  [39] blob_1.2.4                  highr_0.11                 </span></span>
-<span><span class="co">#&gt;  [41] DelayedArray_0.30.1         BiocParallel_1.38.0        </span></span>
-<span><span class="co">#&gt;  [43] prettyunits_1.2.0           parallel_4.4.0             </span></span>
-<span><span class="co">#&gt;  [45] cluster_2.1.6               R6_2.5.1                   </span></span>
-<span><span class="co">#&gt;  [47] bslib_0.7.0                 stringi_1.8.4              </span></span>
-<span><span class="co">#&gt;  [49] RColorBrewer_1.1-3          limma_3.60.3               </span></span>
-<span><span class="co">#&gt;  [51] brio_1.1.5                  jquerylib_0.1.4            </span></span>
-<span><span class="co">#&gt;  [53] Rcpp_1.0.12                 bookdown_0.40              </span></span>
-<span><span class="co">#&gt;  [55] assertthat_0.2.1            iterators_1.0.14           </span></span>
-<span><span class="co">#&gt;  [57] knitr_1.47                  Matrix_1.7-0               </span></span>
-<span><span class="co">#&gt;  [59] tidyselect_1.2.1            abind_1.4-5                </span></span>
-<span><span class="co">#&gt;  [61] yaml_2.3.9                  doParallel_1.0.17          </span></span>
-<span><span class="co">#&gt;  [63] codetools_0.2-20            curl_5.2.1                 </span></span>
-<span><span class="co">#&gt;  [65] lattice_0.22-6              tibble_3.2.1               </span></span>
-<span><span class="co">#&gt;  [67] KEGGREST_1.44.1             withr_3.0.0                </span></span>
-<span><span class="co">#&gt;  [69] evaluate_0.24.0             desc_1.4.3                 </span></span>
-<span><span class="co">#&gt;  [71] BiocFileCache_2.12.0        xml2_1.3.6                 </span></span>
-<span><span class="co">#&gt;  [73] Biostrings_2.72.1           circlize_0.4.16            </span></span>
-<span><span class="co">#&gt;  [75] filelock_1.0.3              pillar_1.9.0               </span></span>
-<span><span class="co">#&gt;  [77] BiocManager_1.30.23         checkmate_2.3.1            </span></span>
-<span><span class="co">#&gt;  [79] foreach_1.5.2               generics_0.1.3             </span></span>
-<span><span class="co">#&gt;  [81] hms_1.1.3                   munsell_0.5.1              </span></span>
-<span><span class="co">#&gt;  [83] scales_1.3.0                glue_1.7.0                 </span></span>
-<span><span class="co">#&gt;  [85] tools_4.4.0                 locfit_1.5-9.10            </span></span>
-<span><span class="co">#&gt;  [87] forcats_1.0.0               fs_1.6.4                   </span></span>
-<span><span class="co">#&gt;  [89] grid_4.4.0                  tidyr_1.3.1                </span></span>
-<span><span class="co">#&gt;  [91] rbibutils_2.2.16            edgeR_4.2.0                </span></span>
-<span><span class="co">#&gt;  [93] AnnotationDbi_1.66.0        colorspace_2.1-0           </span></span>
-<span><span class="co">#&gt;  [95] GenomeInfoDbData_1.2.12     cli_3.6.3                  </span></span>
-<span><span class="co">#&gt;  [97] rappdirs_0.3.3              textshaping_0.4.0          </span></span>
-<span><span class="co">#&gt;  [99] fansi_1.0.6                 S4Arrays_1.4.1             </span></span>
-<span><span class="co">#&gt; [101] ComplexHeatmap_2.20.0       dplyr_1.1.4                </span></span>
-<span><span class="co">#&gt; [103] gtable_0.3.5                DESeq2_1.44.0              </span></span>
-<span><span class="co">#&gt; [105] sass_0.4.9                  digest_0.6.36              </span></span>
-<span><span class="co">#&gt; [107] SparseArray_1.4.8           ggrepel_0.9.5              </span></span>
-<span><span class="co">#&gt; [109] farver_2.1.2                rjson_0.2.21               </span></span>
-<span><span class="co">#&gt; [111] htmlwidgets_1.6.4           memoise_2.0.1              </span></span>
-<span><span class="co">#&gt; [113] htmltools_0.5.8.1           pkgdown_2.0.9              </span></span>
-<span><span class="co">#&gt; [115] lifecycle_1.0.4             httr_1.4.7                 </span></span>
-<span><span class="co">#&gt; [117] statmod_1.5.0               GlobalOptions_0.1.2        </span></span>
-<span><span class="co">#&gt; [119] bit64_4.0.5</span></span></code></pre>
-</div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+<span><span class="co">#&gt;  [27] rmarkdown_2.29              UCSC.utils_1.2.0           </span></span>
+<span><span class="co">#&gt;  [29] ragg_1.3.3                  purrr_1.0.2                </span></span>
+<span><span class="co">#&gt;  [31] bit_4.5.0.1                 xfun_0.49                  </span></span>
+<span><span class="co">#&gt;  [33] MultiAssayExperiment_1.32.0 zlibbioc_1.52.0            </span></span>
+<span><span class="co">#&gt;  [35] cachem_1.1.0                jsonlite_1.8.9             </span></span>
+<span><span class="co">#&gt;  [37] progress_1.2.3              EnvStats_3.0.0             </span></span>
+<span><span class="co">#&gt;  [39] blob_1.2.4                  DelayedArray_0.32.0        </span></span>
+<span><span class="co">#&gt;  [41] BiocParallel_1.40.0         prettyunits_1.2.0          </span></span>
+<span><span class="co">#&gt;  [43] parallel_4.4.1              cluster_2.1.8              </span></span>
+<span><span class="co">#&gt;  [45] R6_2.5.1                    bslib_0.8.0                </span></span>
+<span><span class="co">#&gt;  [47] stringi_1.8.4               RColorBrewer_1.1-3         </span></span>
+<span><span class="co">#&gt;  [49] limma_3.62.1                brio_1.1.5                 </span></span>
+<span><span class="co">#&gt;  [51] jquerylib_0.1.4             Rcpp_1.0.13-1              </span></span>
+<span><span class="co">#&gt;  [53] bookdown_0.41               assertthat_0.2.1           </span></span>
+<span><span class="co">#&gt;  [55] iterators_1.0.14            knitr_1.49                 </span></span>
+<span><span class="co">#&gt;  [57] Matrix_1.7-1                tidyselect_1.2.1           </span></span>
+<span><span class="co">#&gt;  [59] abind_1.4-8                 yaml_2.3.10                </span></span>
+<span><span class="co">#&gt;  [61] doParallel_1.0.17           codetools_0.2-20           </span></span>
+<span><span class="co">#&gt;  [63] curl_6.0.1                  lattice_0.22-6             </span></span>
+<span><span class="co">#&gt;  [65] tibble_3.2.1                KEGGREST_1.46.0            </span></span>
+<span><span class="co">#&gt;  [67] withr_3.0.2                 evaluate_1.0.1             </span></span>
+<span><span class="co">#&gt;  [69] desc_1.4.3                  BiocFileCache_2.14.0       </span></span>
+<span><span class="co">#&gt;  [71] xml2_1.3.6                  Biostrings_2.74.0          </span></span>
+<span><span class="co">#&gt;  [73] circlize_0.4.16             filelock_1.0.3             </span></span>
+<span><span class="co">#&gt;  [75] pillar_1.9.0                BiocManager_1.30.25        </span></span>
+<span><span class="co">#&gt;  [77] checkmate_2.3.2             foreach_1.5.2              </span></span>
+<span><span class="co">#&gt;  [79] generics_0.1.3              hms_1.1.3                  </span></span>
+<span><span class="co">#&gt;  [81] munsell_0.5.1               scales_1.3.0               </span></span>
+<span><span class="co">#&gt;  [83] glue_1.8.0                  tools_4.4.1                </span></span>
+<span><span class="co">#&gt;  [85] locfit_1.5-9.10             forcats_1.0.0              </span></span>
+<span><span class="co">#&gt;  [87] fs_1.6.5                    grid_4.4.1                 </span></span>
+<span><span class="co">#&gt;  [89] tidyr_1.3.1                 rbibutils_2.3              </span></span>
+<span><span class="co">#&gt;  [91] edgeR_4.4.1                 AnnotationDbi_1.68.0       </span></span>
+<span><span class="co">#&gt;  [93] colorspace_2.1-1            GenomeInfoDbData_1.2.13    </span></span>
+<span><span class="co">#&gt;  [95] cli_3.6.3                   rappdirs_0.3.3             </span></span>
+<span><span class="co">#&gt;  [97] textshaping_0.4.0           fansi_1.0.6                </span></span>
+<span><span class="co">#&gt;  [99] S4Arrays_1.6.0              ComplexHeatmap_2.22.0      </span></span>
+<span><span class="co">#&gt; [101] dplyr_1.1.4                 gtable_0.3.6               </span></span>
+<span><span class="co">#&gt; [103] DESeq2_1.46.0               sass_0.4.9                 </span></span>
+<span><span class="co">#&gt; [105] digest_0.6.37               SparseArray_1.6.0          </span></span>
+<span><span class="co">#&gt; [107] ggrepel_0.9.6               farver_2.1.2               </span></span>
+<span><span class="co">#&gt; [109] rjson_0.2.23                htmlwidgets_1.6.4          </span></span>
+<span><span class="co">#&gt; [111] memoise_2.0.1               htmltools_0.5.8.1          </span></span>
+<span><span class="co">#&gt; [113] pkgdown_2.1.1               lifecycle_1.0.4            </span></span>
+<span><span class="co">#&gt; [115] httr_1.4.7                  statmod_1.5.0              </span></span>
+<span><span class="co">#&gt; [117] GlobalOptions_0.1.2         bit64_4.5.2</span></span></code></pre>
+</div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -914,15 +868,15 @@ <h2 class="unnumbered" id="session-info">Session Info<a class="anchor" aria-labe
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/main/articles/hermes_files/figure-html/unnamed-chunk-39-1.png b/main/articles/hermes_files/figure-html/unnamed-chunk-39-1.png
index 9cb437d4..23bc65e8 100644
Binary files a/main/articles/hermes_files/figure-html/unnamed-chunk-39-1.png and b/main/articles/hermes_files/figure-html/unnamed-chunk-39-1.png differ
diff --git a/main/articles/index.html b/main/articles/index.html
index 63c34e36..122e257e 100644
--- a/main/articles/index.html
+++ b/main/articles/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,49 +7,27 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-article-index">
 <div class="row">
@@ -75,14 +50,14 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/authors.html b/main/authors.html
index be9d03a3..4d00d014 100644
--- a/main/authors.html
+++ b/main/authors.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • hermes</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,49 +7,27 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-citation-authors">
 <div class="row">
@@ -60,92 +35,93 @@
       <img src="logo.png" class="logo" alt=""><h1>Authors and Citation</h1>
     </div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2>Authors</h2>
-      
+
       <ul class="list-unstyled"><li>
-          <p><strong>Daniel Sabanés Bové</strong>. Author, maintainer. 
+          <p><strong>Daniel Sabanés Bové</strong>. Author, maintainer.
           </p>
         </li>
         <li>
-          <p><strong>Namrata Bhatia</strong>. Author. 
+          <p><strong>Namrata Bhatia</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Stefanie Bienert</strong>. Author. 
+          <p><strong>Stefanie Bienert</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Benoit Falquet</strong>. Author. 
+          <p><strong>Benoit Falquet</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Haocheng Li</strong>. Author. 
+          <p><strong>Haocheng Li</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Jeff Luong</strong>. Author. 
+          <p><strong>Jeff Luong</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Lyndsee Midori Zhang</strong>. Author. 
+          <p><strong>Lyndsee Midori Zhang</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Alex Richardson</strong>. Author. 
+          <p><strong>Alex Richardson</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Simona Rossomanno</strong>. Author. 
+          <p><strong>Simona Rossomanno</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Tim Treis</strong>. Author. 
+          <p><strong>Tim Treis</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Mark Yan</strong>. Author. 
+          <p><strong>Mark Yan</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Naomi Chang</strong>. Author. 
+          <p><strong>Naomi Chang</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Chendi Liao</strong>. Author. 
+          <p><strong>Chendi Liao</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Carolyn Zhang</strong>. Author. 
+          <p><strong>Carolyn Zhang</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>Joseph N. Paulson</strong>. Author. 
+          <p><strong>Joseph N. Paulson</strong>. Author.
           </p>
         </li>
         <li>
-          <p><strong>F. Hoffmann-La Roche AG</strong>. Copyright holder, funder. 
+          <p><strong>F. Hoffmann-La Roche AG</strong>. Copyright holder, funder.
           </p>
         </li>
       </ul></div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2 id="citation">Citation</h2>
-      <p><small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
       <p>Sabanés Bové D, Bhatia N, Bienert S, Falquet B, Li H, Luong J, Midori Zhang L, Richardson A, Rossomanno S, Treis T, Yan M, Chang N, Liao C, Carolyn Zhang, Paulson J (2024).
 <em>hermes: Preprocessing, analyzing, and reporting of RNA-seq data</em>.
-R package version 1.7.2.9000, <a href="https://insightsengineering.github.io/hermes/">https://insightsengineering.github.io/hermes/</a>. 
+R package version 1.7.2.9003, <a href="https://insightsengineering.github.io/hermes/">https://insightsengineering.github.io/hermes/</a>.
 </p>
       <pre>@Manual{,
   title = {hermes: Preprocessing, analyzing, and reporting of RNA-seq data},
   author = {Daniel {Sabanés Bové} and Namrata Bhatia and Stefanie Bienert and Benoit Falquet and Haocheng Li and Jeff Luong and Lyndsee {Midori Zhang} and Alex Richardson and Simona Rossomanno and Tim Treis and Mark Yan and Naomi Chang and Chendi Liao and {Carolyn Zhang} and Joseph N. Paulson},
   year = {2024},
-  note = {R package version 1.7.2.9000},
+  note = {R package version 1.7.2.9003},
   url = {https://insightsengineering.github.io/hermes/},
 }</pre>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -154,14 +130,14 @@ <h2 id="citation">Citation</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
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diff --git a/main/deps/bootstrap-5.3.1/bootstrap.min.css b/main/deps/bootstrap-5.3.1/bootstrap.min.css
index 8c093225..3b709d45 100644
--- a/main/deps/bootstrap-5.3.1/bootstrap.min.css
+++ b/main/deps/bootstrap-5.3.1/bootstrap.min.css
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auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) 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var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2313425c'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #97d2f3;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(47,164,231,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media 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reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2382c8f1'%3e%3cpath 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(47,164,231,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #2fa4e7;--bs-pagination-active-border-color: #2fa4e7;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #2fa4e7;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #2fa4e7;--bs-list-group-active-border-color: #2fa4e7;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid 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var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 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var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' 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var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 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auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) 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var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2313425c'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #97d2f3;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(47,164,231,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media 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reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2382c8f1'%3e%3cpath 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(47,164,231,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #2fa4e7;--bs-pagination-active-border-color: #2fa4e7;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #2fa4e7;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #2fa4e7;--bs-list-group-active-border-color: #2fa4e7;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid 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var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 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var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' 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var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 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diff --git a/main/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js b/main/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
new file mode 100644
index 00000000..c628326a
--- /dev/null
+++ b/main/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap Table of Contents v1.0.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+!function(a){"use strict";window.Toc={helpers:{findOrFilter:function(e,t){var n=e.find(t);return e.filter(t).add(n).filter(":not([data-toc-skip])")},generateUniqueIdBase:function(e){return a(e).text().trim().replace(/\'/gi,"").replace(/[& +$,:;=?@"#{}|^~[`%!'<>\]\.\/\(\)\*\\\n\t\b\v]/g,"-").replace(/-{2,}/g,"-").substring(0,64).replace(/^-+|-+$/gm,"").toLowerCase()||e.tagName.toLowerCase()},generateUniqueId:function(e){for(var t=this.generateUniqueIdBase(e),n=0;;n++){var r=t;if(0<n&&(r+="-"+n),!document.getElementById(r))return r}},generateAnchor:function(e){if(e.id)return e.id;var t=this.generateUniqueId(e);return e.id=t},createNavList:function(){return a('<ul class="nav navbar-nav"></ul>')},createChildNavList:function(e){var t=this.createNavList();return e.append(t),t},generateNavEl:function(e,t){var n=a('<a class="nav-link"></a>');n.attr("href","#"+e),n.text(t);var r=a("<li></li>");return r.append(n),r},generateNavItem:function(e){var t=this.generateAnchor(e),n=a(e),r=n.data("toc-text")||n.text();return this.generateNavEl(t,r)},getTopLevel:function(e){for(var t=1;t<=6;t++){if(1<this.findOrFilter(e,"h"+t).length)return t}return 1},getHeadings:function(e,t){var n="h"+t,r="h"+(t+1);return this.findOrFilter(e,n+","+r)},getNavLevel:function(e){return parseInt(e.tagName.charAt(1),10)},populateNav:function(r,a,e){var i,s=r,c=this;e.each(function(e,t){var n=c.generateNavItem(t);c.getNavLevel(t)===a?s=r:i&&s===r&&(s=c.createChildNavList(i)),s.append(n),i=n})},parseOps:function(e){var t;return(t=e.jquery?{$nav:e}:e).$scope=t.$scope||a(document.body),t}},init:function(e){(e=this.helpers.parseOps(e)).$nav.attr("data-toggle","toc");var t=this.helpers.createChildNavList(e.$nav),n=this.helpers.getTopLevel(e.$scope),r=this.helpers.getHeadings(e.$scope,n);this.helpers.populateNav(t,n,r)}},a(function(){a('nav[data-toggle="toc"]').each(function(e,t){var n=a(t);Toc.init(n)})})}(jQuery);
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diff --git a/main/deps/clipboard.js-2.0.11/clipboard.min.js b/main/deps/clipboard.js-2.0.11/clipboard.min.js
new file mode 100644
index 00000000..1103f811
--- /dev/null
+++ b/main/deps/clipboard.js-2.0.11/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.11
+ * https://clipboardjs.com/
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body},n="";return"string"==typeof t?n=o(t,e):t instanceof HTMLInputElement&&!["text","search","url","tel","password"].includes(null==t?void 0:t.type)?n=o(t.value,e):(n=r()(t),c("copy")),n};function l(t){return(l="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var s=function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{},e=t.action,n=void 0===e?"copy":e,o=t.container,e=t.target,t=t.text;if("copy"!==n&&"cut"!==n)throw new Error('Invalid "action" value, use either "copy" or "cut"');if(void 0!==e){if(!e||"object"!==l(e)||1!==e.nodeType)throw new Error('Invalid "target" value, use a valid Element');if("copy"===n&&e.hasAttribute("disabled"))throw new Error('Invalid "target" attribute. 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diff --git a/main/deps/data-deps.txt b/main/deps/data-deps.txt
index 693b82d1..ca4dfd9c 100644
--- a/main/deps/data-deps.txt
+++ b/main/deps/data-deps.txt
@@ -2,3 +2,12 @@
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 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet" />
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script>
+<link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet" />
+<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet" />
+<script src="deps/headroom-0.11.0/headroom.min.js"></script>
+<script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script>
+<script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script>
+<script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script>
+<script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script>
+<script src="deps/search-1.0.0/fuse.min.js"></script>
+<script src="deps/search-1.0.0/mark.min.js"></script>
diff --git a/main/deps/font-awesome-6.5.2/css/all.css b/main/deps/font-awesome-6.5.2/css/all.css
new file mode 100644
index 00000000..151dd57c
--- /dev/null
+++ b/main/deps/font-awesome-6.5.2/css/all.css
@@ -0,0 +1,8028 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
+.fa {
+  font-family: var(--fa-style-family, "Font Awesome 6 Free");
+  font-weight: var(--fa-style, 900); }
+
+.fa,
+.fa-classic,
+.fa-sharp,
+.fas,
+.fa-solid,
+.far,
+.fa-regular,
+.fab,
+.fa-brands {
+  -moz-osx-font-smoothing: grayscale;
+  -webkit-font-smoothing: antialiased;
+  display: var(--fa-display, inline-block);
+  font-style: normal;
+  font-variant: normal;
+  line-height: 1;
+  text-rendering: auto; }
+
+.fas,
+.fa-classic,
+.fa-solid,
+.far,
+.fa-regular {
+  font-family: 'Font Awesome 6 Free'; }
+
+.fab,
+.fa-brands {
+  font-family: 'Font Awesome 6 Brands'; }
+
+.fa-1x {
+  font-size: 1em; }
+
+.fa-2x {
+  font-size: 2em; }
+
+.fa-3x {
+  font-size: 3em; }
+
+.fa-4x {
+  font-size: 4em; }
+
+.fa-5x {
+  font-size: 5em; }
+
+.fa-6x {
+  font-size: 6em; }
+
+.fa-7x {
+  font-size: 7em; }
+
+.fa-8x {
+  font-size: 8em; }
+
+.fa-9x {
+  font-size: 9em; }
+
+.fa-10x {
+  font-size: 10em; }
+
+.fa-2xs {
+  font-size: 0.625em;
+  line-height: 0.1em;
+  vertical-align: 0.225em; }
+
+.fa-xs {
+  font-size: 0.75em;
+  line-height: 0.08333em;
+  vertical-align: 0.125em; }
+
+.fa-sm {
+  font-size: 0.875em;
+  line-height: 0.07143em;
+  vertical-align: 0.05357em; }
+
+.fa-lg {
+  font-size: 1.25em;
+  line-height: 0.05em;
+  vertical-align: -0.075em; }
+
+.fa-xl {
+  font-size: 1.5em;
+  line-height: 0.04167em;
+  vertical-align: -0.125em; }
+
+.fa-2xl {
+  font-size: 2em;
+  line-height: 0.03125em;
+  vertical-align: -0.1875em; }
+
+.fa-fw {
+  text-align: center;
+  width: 1.25em; }
+
+.fa-ul {
+  list-style-type: none;
+  margin-left: var(--fa-li-margin, 2.5em);
+  padding-left: 0; }
+  .fa-ul > li {
+    position: relative; }
+
+.fa-li {
+  left: calc(var(--fa-li-width, 2em) * -1);
+  position: absolute;
+  text-align: center;
+  width: var(--fa-li-width, 2em);
+  line-height: inherit; }
+
+.fa-border {
+  border-color: var(--fa-border-color, #eee);
+  border-radius: var(--fa-border-radius, 0.1em);
+  border-style: var(--fa-border-style, solid);
+  border-width: var(--fa-border-width, 0.08em);
+  padding: var(--fa-border-padding, 0.2em 0.25em 0.15em); }
+
+.fa-pull-left {
+  float: left;
+  margin-right: var(--fa-pull-margin, 0.3em); }
+
+.fa-pull-right {
+  float: right;
+  margin-left: var(--fa-pull-margin, 0.3em); }
+
+.fa-beat {
+  -webkit-animation-name: fa-beat;
+          animation-name: fa-beat;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-bounce {
+  -webkit-animation-name: fa-bounce;
+          animation-name: fa-bounce;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1)); }
+
+.fa-fade {
+  -webkit-animation-name: fa-fade;
+          animation-name: fa-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-beat-fade {
+  -webkit-animation-name: fa-beat-fade;
+          animation-name: fa-beat-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-flip {
+  -webkit-animation-name: fa-flip;
+          animation-name: fa-flip;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-shake {
+  -webkit-animation-name: fa-shake;
+          animation-name: fa-shake;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 2s);
+          animation-duration: var(--fa-animation-duration, 2s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin-reverse {
+  --fa-animation-direction: reverse; }
+
+.fa-pulse,
+.fa-spin-pulse {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, steps(8));
+          animation-timing-function: var(--fa-animation-timing, steps(8)); }
+
+@media (prefers-reduced-motion: reduce) {
+  .fa-beat,
+  .fa-bounce,
+  .fa-fade,
+  .fa-beat-fade,
+  .fa-flip,
+  .fa-pulse,
+  .fa-shake,
+  .fa-spin,
+  .fa-spin-pulse {
+    -webkit-animation-delay: -1ms;
+            animation-delay: -1ms;
+    -webkit-animation-duration: 1ms;
+            animation-duration: 1ms;
+    -webkit-animation-iteration-count: 1;
+            animation-iteration-count: 1;
+    -webkit-transition-delay: 0s;
+            transition-delay: 0s;
+    -webkit-transition-duration: 0s;
+            transition-duration: 0s; } }
+
+@-webkit-keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@-webkit-keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@-webkit-keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@-webkit-keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@-webkit-keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@-webkit-keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@-webkit-keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+@keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+.fa-rotate-90 {
+  -webkit-transform: rotate(90deg);
+          transform: rotate(90deg); }
+
+.fa-rotate-180 {
+  -webkit-transform: rotate(180deg);
+          transform: rotate(180deg); }
+
+.fa-rotate-270 {
+  -webkit-transform: rotate(270deg);
+          transform: rotate(270deg); }
+
+.fa-flip-horizontal {
+  -webkit-transform: scale(-1, 1);
+          transform: scale(-1, 1); }
+
+.fa-flip-vertical {
+  -webkit-transform: scale(1, -1);
+          transform: scale(1, -1); }
+
+.fa-flip-both,
+.fa-flip-horizontal.fa-flip-vertical {
+  -webkit-transform: scale(-1, -1);
+          transform: scale(-1, -1); }
+
+.fa-rotate-by {
+  -webkit-transform: rotate(var(--fa-rotate-angle, 0));
+          transform: rotate(var(--fa-rotate-angle, 0)); }
+
+.fa-stack {
+  display: inline-block;
+  height: 2em;
+  line-height: 2em;
+  position: relative;
+  vertical-align: middle;
+  width: 2.5em; }
+
+.fa-stack-1x,
+.fa-stack-2x {
+  left: 0;
+  position: absolute;
+  text-align: center;
+  width: 100%;
+  z-index: var(--fa-stack-z-index, auto); }
+
+.fa-stack-1x {
+  line-height: inherit; }
+
+.fa-stack-2x {
+  font-size: 2em; }
+
+.fa-inverse {
+  color: var(--fa-inverse, #fff); }
+
+/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen
+readers do not read off random characters that represent icons */
+
+.fa-0::before {
+  content: "\30"; }
+
+.fa-1::before {
+  content: "\31"; }
+
+.fa-2::before {
+  content: "\32"; }
+
+.fa-3::before {
+  content: "\33"; }
+
+.fa-4::before {
+  content: "\34"; }
+
+.fa-5::before {
+  content: "\35"; }
+
+.fa-6::before {
+  content: "\36"; }
+
+.fa-7::before {
+  content: "\37"; }
+
+.fa-8::before {
+  content: "\38"; }
+
+.fa-9::before {
+  content: "\39"; }
+
+.fa-fill-drip::before {
+  content: "\f576"; }
+
+.fa-arrows-to-circle::before {
+  content: "\e4bd"; }
+
+.fa-circle-chevron-right::before {
+  content: "\f138"; }
+
+.fa-chevron-circle-right::before {
+  content: "\f138"; }
+
+.fa-at::before {
+  content: "\40"; }
+
+.fa-trash-can::before {
+  content: "\f2ed"; }
+
+.fa-trash-alt::before {
+  content: "\f2ed"; }
+
+.fa-text-height::before {
+  content: "\f034"; }
+
+.fa-user-xmark::before {
+  content: "\f235"; }
+
+.fa-user-times::before {
+  content: "\f235"; }
+
+.fa-stethoscope::before {
+  content: "\f0f1"; }
+
+.fa-message::before {
+  content: "\f27a"; }
+
+.fa-comment-alt::before {
+  content: "\f27a"; }
+
+.fa-info::before {
+  content: "\f129"; }
+
+.fa-down-left-and-up-right-to-center::before {
+  content: "\f422"; }
+
+.fa-compress-alt::before {
+  content: "\f422"; }
+
+.fa-explosion::before {
+  content: "\e4e9"; }
+
+.fa-file-lines::before {
+  content: "\f15c"; }
+
+.fa-file-alt::before {
+  content: "\f15c"; }
+
+.fa-file-text::before {
+  content: "\f15c"; }
+
+.fa-wave-square::before {
+  content: "\f83e"; }
+
+.fa-ring::before {
+  content: "\f70b"; }
+
+.fa-building-un::before {
+  content: "\e4d9"; }
+
+.fa-dice-three::before {
+  content: "\f527"; }
+
+.fa-calendar-days::before {
+  content: "\f073"; }
+
+.fa-calendar-alt::before {
+  content: "\f073"; }
+
+.fa-anchor-circle-check::before {
+  content: "\e4aa"; }
+
+.fa-building-circle-arrow-right::before {
+  content: "\e4d1"; }
+
+.fa-volleyball::before {
+  content: "\f45f"; }
+
+.fa-volleyball-ball::before {
+  content: "\f45f"; }
+
+.fa-arrows-up-to-line::before {
+  content: "\e4c2"; }
+
+.fa-sort-down::before {
+  content: "\f0dd"; }
+
+.fa-sort-desc::before {
+  content: "\f0dd"; }
+
+.fa-circle-minus::before {
+  content: "\f056"; }
+
+.fa-minus-circle::before {
+  content: "\f056"; }
+
+.fa-door-open::before {
+  content: "\f52b"; }
+
+.fa-right-from-bracket::before {
+  content: "\f2f5"; }
+
+.fa-sign-out-alt::before {
+  content: "\f2f5"; }
+
+.fa-atom::before {
+  content: "\f5d2"; }
+
+.fa-soap::before {
+  content: "\e06e"; }
+
+.fa-icons::before {
+  content: "\f86d"; }
+
+.fa-heart-music-camera-bolt::before {
+  content: "\f86d"; }
+
+.fa-microphone-lines-slash::before {
+  content: "\f539"; }
+
+.fa-microphone-alt-slash::before {
+  content: "\f539"; }
+
+.fa-bridge-circle-check::before {
+  content: "\e4c9"; }
+
+.fa-pump-medical::before {
+  content: "\e06a"; }
+
+.fa-fingerprint::before {
+  content: "\f577"; }
+
+.fa-hand-point-right::before {
+  content: "\f0a4"; }
+
+.fa-magnifying-glass-location::before {
+  content: "\f689"; }
+
+.fa-search-location::before {
+  content: "\f689"; }
+
+.fa-forward-step::before {
+  content: "\f051"; }
+
+.fa-step-forward::before {
+  content: "\f051"; }
+
+.fa-face-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-flag-checkered::before {
+  content: "\f11e"; }
+
+.fa-football::before {
+  content: "\f44e"; }
+
+.fa-football-ball::before {
+  content: "\f44e"; }
+
+.fa-school-circle-exclamation::before {
+  content: "\e56c"; }
+
+.fa-crop::before {
+  content: "\f125"; }
+
+.fa-angles-down::before {
+  content: "\f103"; }
+
+.fa-angle-double-down::before {
+  content: "\f103"; }
+
+.fa-users-rectangle::before {
+  content: "\e594"; }
+
+.fa-people-roof::before {
+  content: "\e537"; }
+
+.fa-people-line::before {
+  content: "\e534"; }
+
+.fa-beer-mug-empty::before {
+  content: "\f0fc"; }
+
+.fa-beer::before {
+  content: "\f0fc"; }
+
+.fa-diagram-predecessor::before {
+  content: "\e477"; }
+
+.fa-arrow-up-long::before {
+  content: "\f176"; }
+
+.fa-long-arrow-up::before {
+  content: "\f176"; }
+
+.fa-fire-flame-simple::before {
+  content: "\f46a"; }
+
+.fa-burn::before {
+  content: "\f46a"; }
+
+.fa-person::before {
+  content: "\f183"; }
+
+.fa-male::before {
+  content: "\f183"; }
+
+.fa-laptop::before {
+  content: "\f109"; }
+
+.fa-file-csv::before {
+  content: "\f6dd"; }
+
+.fa-menorah::before {
+  content: "\f676"; }
+
+.fa-truck-plane::before {
+  content: "\e58f"; }
+
+.fa-record-vinyl::before {
+  content: "\f8d9"; }
+
+.fa-face-grin-stars::before {
+  content: "\f587"; }
+
+.fa-grin-stars::before {
+  content: "\f587"; }
+
+.fa-bong::before {
+  content: "\f55c"; }
+
+.fa-spaghetti-monster-flying::before {
+  content: "\f67b"; }
+
+.fa-pastafarianism::before {
+  content: "\f67b"; }
+
+.fa-arrow-down-up-across-line::before {
+  content: "\e4af"; }
+
+.fa-spoon::before {
+  content: "\f2e5"; }
+
+.fa-utensil-spoon::before {
+  content: "\f2e5"; }
+
+.fa-jar-wheat::before {
+  content: "\e517"; }
+
+.fa-envelopes-bulk::before {
+  content: "\f674"; }
+
+.fa-mail-bulk::before {
+  content: "\f674"; }
+
+.fa-file-circle-exclamation::before {
+  content: "\e4eb"; }
+
+.fa-circle-h::before {
+  content: "\f47e"; }
+
+.fa-hospital-symbol::before {
+  content: "\f47e"; }
+
+.fa-pager::before {
+  content: "\f815"; }
+
+.fa-address-book::before {
+  content: "\f2b9"; }
+
+.fa-contact-book::before {
+  content: "\f2b9"; }
+
+.fa-strikethrough::before {
+  content: "\f0cc"; }
+
+.fa-k::before {
+  content: "\4b"; }
+
+.fa-landmark-flag::before {
+  content: "\e51c"; }
+
+.fa-pencil::before {
+  content: "\f303"; }
+
+.fa-pencil-alt::before {
+  content: "\f303"; }
+
+.fa-backward::before {
+  content: "\f04a"; }
+
+.fa-caret-right::before {
+  content: "\f0da"; }
+
+.fa-comments::before {
+  content: "\f086"; }
+
+.fa-paste::before {
+  content: "\f0ea"; }
+
+.fa-file-clipboard::before {
+  content: "\f0ea"; }
+
+.fa-code-pull-request::before {
+  content: "\e13c"; }
+
+.fa-clipboard-list::before {
+  content: "\f46d"; }
+
+.fa-truck-ramp-box::before {
+  content: "\f4de"; }
+
+.fa-truck-loading::before {
+  content: "\f4de"; }
+
+.fa-user-check::before {
+  content: "\f4fc"; }
+
+.fa-vial-virus::before {
+  content: "\e597"; }
+
+.fa-sheet-plastic::before {
+  content: "\e571"; }
+
+.fa-blog::before {
+  content: "\f781"; }
+
+.fa-user-ninja::before {
+  content: "\f504"; }
+
+.fa-person-arrow-up-from-line::before {
+  content: "\e539"; }
+
+.fa-scroll-torah::before {
+  content: "\f6a0"; }
+
+.fa-torah::before {
+  content: "\f6a0"; }
+
+.fa-broom-ball::before {
+  content: "\f458"; }
+
+.fa-quidditch::before {
+  content: "\f458"; }
+
+.fa-quidditch-broom-ball::before {
+  content: "\f458"; }
+
+.fa-toggle-off::before {
+  content: "\f204"; }
+
+.fa-box-archive::before {
+  content: "\f187"; }
+
+.fa-archive::before {
+  content: "\f187"; }
+
+.fa-person-drowning::before {
+  content: "\e545"; }
+
+.fa-arrow-down-9-1::before {
+  content: "\f886"; }
+
+.fa-sort-numeric-desc::before {
+  content: "\f886"; }
+
+.fa-sort-numeric-down-alt::before {
+  content: "\f886"; }
+
+.fa-face-grin-tongue-squint::before {
+  content: "\f58a"; }
+
+.fa-grin-tongue-squint::before {
+  content: "\f58a"; }
+
+.fa-spray-can::before {
+  content: "\f5bd"; }
+
+.fa-truck-monster::before {
+  content: "\f63b"; }
+
+.fa-w::before {
+  content: "\57"; }
+
+.fa-earth-africa::before {
+  content: "\f57c"; }
+
+.fa-globe-africa::before {
+  content: "\f57c"; }
+
+.fa-rainbow::before {
+  content: "\f75b"; }
+
+.fa-circle-notch::before {
+  content: "\f1ce"; }
+
+.fa-tablet-screen-button::before {
+  content: "\f3fa"; }
+
+.fa-tablet-alt::before {
+  content: "\f3fa"; }
+
+.fa-paw::before {
+  content: "\f1b0"; }
+
+.fa-cloud::before {
+  content: "\f0c2"; }
+
+.fa-trowel-bricks::before {
+  content: "\e58a"; }
+
+.fa-face-flushed::before {
+  content: "\f579"; }
+
+.fa-flushed::before {
+  content: "\f579"; }
+
+.fa-hospital-user::before {
+  content: "\f80d"; }
+
+.fa-tent-arrow-left-right::before {
+  content: "\e57f"; }
+
+.fa-gavel::before {
+  content: "\f0e3"; }
+
+.fa-legal::before {
+  content: "\f0e3"; }
+
+.fa-binoculars::before {
+  content: "\f1e5"; }
+
+.fa-microphone-slash::before {
+  content: "\f131"; }
+
+.fa-box-tissue::before {
+  content: "\e05b"; }
+
+.fa-motorcycle::before {
+  content: "\f21c"; }
+
+.fa-bell-concierge::before {
+  content: "\f562"; }
+
+.fa-concierge-bell::before {
+  content: "\f562"; }
+
+.fa-pen-ruler::before {
+  content: "\f5ae"; }
+
+.fa-pencil-ruler::before {
+  content: "\f5ae"; }
+
+.fa-people-arrows::before {
+  content: "\e068"; }
+
+.fa-people-arrows-left-right::before {
+  content: "\e068"; }
+
+.fa-mars-and-venus-burst::before {
+  content: "\e523"; }
+
+.fa-square-caret-right::before {
+  content: "\f152"; }
+
+.fa-caret-square-right::before {
+  content: "\f152"; }
+
+.fa-scissors::before {
+  content: "\f0c4"; }
+
+.fa-cut::before {
+  content: "\f0c4"; }
+
+.fa-sun-plant-wilt::before {
+  content: "\e57a"; }
+
+.fa-toilets-portable::before {
+  content: "\e584"; }
+
+.fa-hockey-puck::before {
+  content: "\f453"; }
+
+.fa-table::before {
+  content: "\f0ce"; }
+
+.fa-magnifying-glass-arrow-right::before {
+  content: "\e521"; }
+
+.fa-tachograph-digital::before {
+  content: "\f566"; }
+
+.fa-digital-tachograph::before {
+  content: "\f566"; }
+
+.fa-users-slash::before {
+  content: "\e073"; }
+
+.fa-clover::before {
+  content: "\e139"; }
+
+.fa-reply::before {
+  content: "\f3e5"; }
+
+.fa-mail-reply::before {
+  content: "\f3e5"; }
+
+.fa-star-and-crescent::before {
+  content: "\f699"; }
+
+.fa-house-fire::before {
+  content: "\e50c"; }
+
+.fa-square-minus::before {
+  content: "\f146"; }
+
+.fa-minus-square::before {
+  content: "\f146"; }
+
+.fa-helicopter::before {
+  content: "\f533"; }
+
+.fa-compass::before {
+  content: "\f14e"; }
+
+.fa-square-caret-down::before {
+  content: "\f150"; }
+
+.fa-caret-square-down::before {
+  content: "\f150"; }
+
+.fa-file-circle-question::before {
+  content: "\e4ef"; }
+
+.fa-laptop-code::before {
+  content: "\f5fc"; }
+
+.fa-swatchbook::before {
+  content: "\f5c3"; }
+
+.fa-prescription-bottle::before {
+  content: "\f485"; }
+
+.fa-bars::before {
+  content: "\f0c9"; }
+
+.fa-navicon::before {
+  content: "\f0c9"; }
+
+.fa-people-group::before {
+  content: "\e533"; }
+
+.fa-hourglass-end::before {
+  content: "\f253"; }
+
+.fa-hourglass-3::before {
+  content: "\f253"; }
+
+.fa-heart-crack::before {
+  content: "\f7a9"; }
+
+.fa-heart-broken::before {
+  content: "\f7a9"; }
+
+.fa-square-up-right::before {
+  content: "\f360"; }
+
+.fa-external-link-square-alt::before {
+  content: "\f360"; }
+
+.fa-face-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-film::before {
+  content: "\f008"; }
+
+.fa-ruler-horizontal::before {
+  content: "\f547"; }
+
+.fa-people-robbery::before {
+  content: "\e536"; }
+
+.fa-lightbulb::before {
+  content: "\f0eb"; }
+
+.fa-caret-left::before {
+  content: "\f0d9"; }
+
+.fa-circle-exclamation::before {
+  content: "\f06a"; }
+
+.fa-exclamation-circle::before {
+  content: "\f06a"; }
+
+.fa-school-circle-xmark::before {
+  content: "\e56d"; }
+
+.fa-arrow-right-from-bracket::before {
+  content: "\f08b"; }
+
+.fa-sign-out::before {
+  content: "\f08b"; }
+
+.fa-circle-chevron-down::before {
+  content: "\f13a"; }
+
+.fa-chevron-circle-down::before {
+  content: "\f13a"; }
+
+.fa-unlock-keyhole::before {
+  content: "\f13e"; }
+
+.fa-unlock-alt::before {
+  content: "\f13e"; }
+
+.fa-cloud-showers-heavy::before {
+  content: "\f740"; }
+
+.fa-headphones-simple::before {
+  content: "\f58f"; }
+
+.fa-headphones-alt::before {
+  content: "\f58f"; }
+
+.fa-sitemap::before {
+  content: "\f0e8"; }
+
+.fa-circle-dollar-to-slot::before {
+  content: "\f4b9"; }
+
+.fa-donate::before {
+  content: "\f4b9"; }
+
+.fa-memory::before {
+  content: "\f538"; }
+
+.fa-road-spikes::before {
+  content: "\e568"; }
+
+.fa-fire-burner::before {
+  content: "\e4f1"; }
+
+.fa-flag::before {
+  content: "\f024"; }
+
+.fa-hanukiah::before {
+  content: "\f6e6"; }
+
+.fa-feather::before {
+  content: "\f52d"; }
+
+.fa-volume-low::before {
+  content: "\f027"; }
+
+.fa-volume-down::before {
+  content: "\f027"; }
+
+.fa-comment-slash::before {
+  content: "\f4b3"; }
+
+.fa-cloud-sun-rain::before {
+  content: "\f743"; }
+
+.fa-compress::before {
+  content: "\f066"; }
+
+.fa-wheat-awn::before {
+  content: "\e2cd"; }
+
+.fa-wheat-alt::before {
+  content: "\e2cd"; }
+
+.fa-ankh::before {
+  content: "\f644"; }
+
+.fa-hands-holding-child::before {
+  content: "\e4fa"; }
+
+.fa-asterisk::before {
+  content: "\2a"; }
+
+.fa-square-check::before {
+  content: "\f14a"; }
+
+.fa-check-square::before {
+  content: "\f14a"; }
+
+.fa-peseta-sign::before {
+  content: "\e221"; }
+
+.fa-heading::before {
+  content: "\f1dc"; }
+
+.fa-header::before {
+  content: "\f1dc"; }
+
+.fa-ghost::before {
+  content: "\f6e2"; }
+
+.fa-list::before {
+  content: "\f03a"; }
+
+.fa-list-squares::before {
+  content: "\f03a"; }
+
+.fa-square-phone-flip::before {
+  content: "\f87b"; }
+
+.fa-phone-square-alt::before {
+  content: "\f87b"; }
+
+.fa-cart-plus::before {
+  content: "\f217"; }
+
+.fa-gamepad::before {
+  content: "\f11b"; }
+
+.fa-circle-dot::before {
+  content: "\f192"; }
+
+.fa-dot-circle::before {
+  content: "\f192"; }
+
+.fa-face-dizzy::before {
+  content: "\f567"; }
+
+.fa-dizzy::before {
+  content: "\f567"; }
+
+.fa-egg::before {
+  content: "\f7fb"; }
+
+.fa-house-medical-circle-xmark::before {
+  content: "\e513"; }
+
+.fa-campground::before {
+  content: "\f6bb"; }
+
+.fa-folder-plus::before {
+  content: "\f65e"; }
+
+.fa-futbol::before {
+  content: "\f1e3"; }
+
+.fa-futbol-ball::before {
+  content: "\f1e3"; }
+
+.fa-soccer-ball::before {
+  content: "\f1e3"; }
+
+.fa-paintbrush::before {
+  content: "\f1fc"; }
+
+.fa-paint-brush::before {
+  content: "\f1fc"; }
+
+.fa-lock::before {
+  content: "\f023"; }
+
+.fa-gas-pump::before {
+  content: "\f52f"; }
+
+.fa-hot-tub-person::before {
+  content: "\f593"; }
+
+.fa-hot-tub::before {
+  content: "\f593"; }
+
+.fa-map-location::before {
+  content: "\f59f"; }
+
+.fa-map-marked::before {
+  content: "\f59f"; }
+
+.fa-house-flood-water::before {
+  content: "\e50e"; }
+
+.fa-tree::before {
+  content: "\f1bb"; }
+
+.fa-bridge-lock::before {
+  content: "\e4cc"; }
+
+.fa-sack-dollar::before {
+  content: "\f81d"; }
+
+.fa-pen-to-square::before {
+  content: "\f044"; }
+
+.fa-edit::before {
+  content: "\f044"; }
+
+.fa-car-side::before {
+  content: "\f5e4"; }
+
+.fa-share-nodes::before {
+  content: "\f1e0"; }
+
+.fa-share-alt::before {
+  content: "\f1e0"; }
+
+.fa-heart-circle-minus::before {
+  content: "\e4ff"; }
+
+.fa-hourglass-half::before {
+  content: "\f252"; }
+
+.fa-hourglass-2::before {
+  content: "\f252"; }
+
+.fa-microscope::before {
+  content: "\f610"; }
+
+.fa-sink::before {
+  content: "\e06d"; }
+
+.fa-bag-shopping::before {
+  content: "\f290"; }
+
+.fa-shopping-bag::before {
+  content: "\f290"; }
+
+.fa-arrow-down-z-a::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-desc::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-down-alt::before {
+  content: "\f881"; }
+
+.fa-mitten::before {
+  content: "\f7b5"; }
+
+.fa-person-rays::before {
+  content: "\e54d"; }
+
+.fa-users::before {
+  content: "\f0c0"; }
+
+.fa-eye-slash::before {
+  content: "\f070"; }
+
+.fa-flask-vial::before {
+  content: "\e4f3"; }
+
+.fa-hand::before {
+  content: "\f256"; }
+
+.fa-hand-paper::before {
+  content: "\f256"; }
+
+.fa-om::before {
+  content: "\f679"; }
+
+.fa-worm::before {
+  content: "\e599"; }
+
+.fa-house-circle-xmark::before {
+  content: "\e50b"; }
+
+.fa-plug::before {
+  content: "\f1e6"; }
+
+.fa-chevron-up::before {
+  content: "\f077"; }
+
+.fa-hand-spock::before {
+  content: "\f259"; }
+
+.fa-stopwatch::before {
+  content: "\f2f2"; }
+
+.fa-face-kiss::before {
+  content: "\f596"; }
+
+.fa-kiss::before {
+  content: "\f596"; }
+
+.fa-bridge-circle-xmark::before {
+  content: "\e4cb"; }
+
+.fa-face-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-chess-bishop::before {
+  content: "\f43a"; }
+
+.fa-face-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-ear-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deafness::before {
+  content: "\f2a4"; }
+
+.fa-hard-of-hearing::before {
+  content: "\f2a4"; }
+
+.fa-road-circle-check::before {
+  content: "\e564"; }
+
+.fa-dice-five::before {
+  content: "\f523"; }
+
+.fa-square-rss::before {
+  content: "\f143"; }
+
+.fa-rss-square::before {
+  content: "\f143"; }
+
+.fa-land-mine-on::before {
+  content: "\e51b"; }
+
+.fa-i-cursor::before {
+  content: "\f246"; }
+
+.fa-stamp::before {
+  content: "\f5bf"; }
+
+.fa-stairs::before {
+  content: "\e289"; }
+
+.fa-i::before {
+  content: "\49"; }
+
+.fa-hryvnia-sign::before {
+  content: "\f6f2"; }
+
+.fa-hryvnia::before {
+  content: "\f6f2"; }
+
+.fa-pills::before {
+  content: "\f484"; }
+
+.fa-face-grin-wide::before {
+  content: "\f581"; }
+
+.fa-grin-alt::before {
+  content: "\f581"; }
+
+.fa-tooth::before {
+  content: "\f5c9"; }
+
+.fa-v::before {
+  content: "\56"; }
+
+.fa-bangladeshi-taka-sign::before {
+  content: "\e2e6"; }
+
+.fa-bicycle::before {
+  content: "\f206"; }
+
+.fa-staff-snake::before {
+  content: "\e579"; }
+
+.fa-rod-asclepius::before {
+  content: "\e579"; }
+
+.fa-rod-snake::before {
+  content: "\e579"; }
+
+.fa-staff-aesculapius::before {
+  content: "\e579"; }
+
+.fa-head-side-cough-slash::before {
+  content: "\e062"; }
+
+.fa-truck-medical::before {
+  content: "\f0f9"; }
+
+.fa-ambulance::before {
+  content: "\f0f9"; }
+
+.fa-wheat-awn-circle-exclamation::before {
+  content: "\e598"; }
+
+.fa-snowman::before {
+  content: "\f7d0"; }
+
+.fa-mortar-pestle::before {
+  content: "\f5a7"; }
+
+.fa-road-barrier::before {
+  content: "\e562"; }
+
+.fa-school::before {
+  content: "\f549"; }
+
+.fa-igloo::before {
+  content: "\f7ae"; }
+
+.fa-joint::before {
+  content: "\f595"; }
+
+.fa-angle-right::before {
+  content: "\f105"; }
+
+.fa-horse::before {
+  content: "\f6f0"; }
+
+.fa-q::before {
+  content: "\51"; }
+
+.fa-g::before {
+  content: "\47"; }
+
+.fa-notes-medical::before {
+  content: "\f481"; }
+
+.fa-temperature-half::before {
+  content: "\f2c9"; }
+
+.fa-temperature-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-half::before {
+  content: "\f2c9"; }
+
+.fa-dong-sign::before {
+  content: "\e169"; }
+
+.fa-capsules::before {
+  content: "\f46b"; }
+
+.fa-poo-storm::before {
+  content: "\f75a"; }
+
+.fa-poo-bolt::before {
+  content: "\f75a"; }
+
+.fa-face-frown-open::before {
+  content: "\f57a"; }
+
+.fa-frown-open::before {
+  content: "\f57a"; }
+
+.fa-hand-point-up::before {
+  content: "\f0a6"; }
+
+.fa-money-bill::before {
+  content: "\f0d6"; }
+
+.fa-bookmark::before {
+  content: "\f02e"; }
+
+.fa-align-justify::before {
+  content: "\f039"; }
+
+.fa-umbrella-beach::before {
+  content: "\f5ca"; }
+
+.fa-helmet-un::before {
+  content: "\e503"; }
+
+.fa-bullseye::before {
+  content: "\f140"; }
+
+.fa-bacon::before {
+  content: "\f7e5"; }
+
+.fa-hand-point-down::before {
+  content: "\f0a7"; }
+
+.fa-arrow-up-from-bracket::before {
+  content: "\e09a"; }
+
+.fa-folder::before {
+  content: "\f07b"; }
+
+.fa-folder-blank::before {
+  content: "\f07b"; }
+
+.fa-file-waveform::before {
+  content: "\f478"; }
+
+.fa-file-medical-alt::before {
+  content: "\f478"; }
+
+.fa-radiation::before {
+  content: "\f7b9"; }
+
+.fa-chart-simple::before {
+  content: "\e473"; }
+
+.fa-mars-stroke::before {
+  content: "\f229"; }
+
+.fa-vial::before {
+  content: "\f492"; }
+
+.fa-gauge::before {
+  content: "\f624"; }
+
+.fa-dashboard::before {
+  content: "\f624"; }
+
+.fa-gauge-med::before {
+  content: "\f624"; }
+
+.fa-tachometer-alt-average::before {
+  content: "\f624"; }
+
+.fa-wand-magic-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-magic-wand-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-e::before {
+  content: "\45"; }
+
+.fa-pen-clip::before {
+  content: "\f305"; }
+
+.fa-pen-alt::before {
+  content: "\f305"; }
+
+.fa-bridge-circle-exclamation::before {
+  content: "\e4ca"; }
+
+.fa-user::before {
+  content: "\f007"; }
+
+.fa-school-circle-check::before {
+  content: "\e56b"; }
+
+.fa-dumpster::before {
+  content: "\f793"; }
+
+.fa-van-shuttle::before {
+  content: "\f5b6"; }
+
+.fa-shuttle-van::before {
+  content: "\f5b6"; }
+
+.fa-building-user::before {
+  content: "\e4da"; }
+
+.fa-square-caret-left::before {
+  content: "\f191"; }
+
+.fa-caret-square-left::before {
+  content: "\f191"; }
+
+.fa-highlighter::before {
+  content: "\f591"; }
+
+.fa-key::before {
+  content: "\f084"; }
+
+.fa-bullhorn::before {
+  content: "\f0a1"; }
+
+.fa-globe::before {
+  content: "\f0ac"; }
+
+.fa-synagogue::before {
+  content: "\f69b"; }
+
+.fa-person-half-dress::before {
+  content: "\e548"; }
+
+.fa-road-bridge::before {
+  content: "\e563"; }
+
+.fa-location-arrow::before {
+  content: "\f124"; }
+
+.fa-c::before {
+  content: "\43"; }
+
+.fa-tablet-button::before {
+  content: "\f10a"; }
+
+.fa-building-lock::before {
+  content: "\e4d6"; }
+
+.fa-pizza-slice::before {
+  content: "\f818"; }
+
+.fa-money-bill-wave::before {
+  content: "\f53a"; }
+
+.fa-chart-area::before {
+  content: "\f1fe"; }
+
+.fa-area-chart::before {
+  content: "\f1fe"; }
+
+.fa-house-flag::before {
+  content: "\e50d"; }
+
+.fa-person-circle-minus::before {
+  content: "\e540"; }
+
+.fa-ban::before {
+  content: "\f05e"; }
+
+.fa-cancel::before {
+  content: "\f05e"; }
+
+.fa-camera-rotate::before {
+  content: "\e0d8"; }
+
+.fa-spray-can-sparkles::before {
+  content: "\f5d0"; }
+
+.fa-air-freshener::before {
+  content: "\f5d0"; }
+
+.fa-star::before {
+  content: "\f005"; }
+
+.fa-repeat::before {
+  content: "\f363"; }
+
+.fa-cross::before {
+  content: "\f654"; }
+
+.fa-box::before {
+  content: "\f466"; }
+
+.fa-venus-mars::before {
+  content: "\f228"; }
+
+.fa-arrow-pointer::before {
+  content: "\f245"; }
+
+.fa-mouse-pointer::before {
+  content: "\f245"; }
+
+.fa-maximize::before {
+  content: "\f31e"; }
+
+.fa-expand-arrows-alt::before {
+  content: "\f31e"; }
+
+.fa-charging-station::before {
+  content: "\f5e7"; }
+
+.fa-shapes::before {
+  content: "\f61f"; }
+
+.fa-triangle-circle-square::before {
+  content: "\f61f"; }
+
+.fa-shuffle::before {
+  content: "\f074"; }
+
+.fa-random::before {
+  content: "\f074"; }
+
+.fa-person-running::before {
+  content: "\f70c"; }
+
+.fa-running::before {
+  content: "\f70c"; }
+
+.fa-mobile-retro::before {
+  content: "\e527"; }
+
+.fa-grip-lines-vertical::before {
+  content: "\f7a5"; }
+
+.fa-spider::before {
+  content: "\f717"; }
+
+.fa-hands-bound::before {
+  content: "\e4f9"; }
+
+.fa-file-invoice-dollar::before {
+  content: "\f571"; }
+
+.fa-plane-circle-exclamation::before {
+  content: "\e556"; }
+
+.fa-x-ray::before {
+  content: "\f497"; }
+
+.fa-spell-check::before {
+  content: "\f891"; }
+
+.fa-slash::before {
+  content: "\f715"; }
+
+.fa-computer-mouse::before {
+  content: "\f8cc"; }
+
+.fa-mouse::before {
+  content: "\f8cc"; }
+
+.fa-arrow-right-to-bracket::before {
+  content: "\f090"; }
+
+.fa-sign-in::before {
+  content: "\f090"; }
+
+.fa-shop-slash::before {
+  content: "\e070"; }
+
+.fa-store-alt-slash::before {
+  content: "\e070"; }
+
+.fa-server::before {
+  content: "\f233"; }
+
+.fa-virus-covid-slash::before {
+  content: "\e4a9"; }
+
+.fa-shop-lock::before {
+  content: "\e4a5"; }
+
+.fa-hourglass-start::before {
+  content: "\f251"; }
+
+.fa-hourglass-1::before {
+  content: "\f251"; }
+
+.fa-blender-phone::before {
+  content: "\f6b6"; }
+
+.fa-building-wheat::before {
+  content: "\e4db"; }
+
+.fa-person-breastfeeding::before {
+  content: "\e53a"; }
+
+.fa-right-to-bracket::before {
+  content: "\f2f6"; }
+
+.fa-sign-in-alt::before {
+  content: "\f2f6"; }
+
+.fa-venus::before {
+  content: "\f221"; }
+
+.fa-passport::before {
+  content: "\f5ab"; }
+
+.fa-heart-pulse::before {
+  content: "\f21e"; }
+
+.fa-heartbeat::before {
+  content: "\f21e"; }
+
+.fa-people-carry-box::before {
+  content: "\f4ce"; }
+
+.fa-people-carry::before {
+  content: "\f4ce"; }
+
+.fa-temperature-high::before {
+  content: "\f769"; }
+
+.fa-microchip::before {
+  content: "\f2db"; }
+
+.fa-crown::before {
+  content: "\f521"; }
+
+.fa-weight-hanging::before {
+  content: "\f5cd"; }
+
+.fa-xmarks-lines::before {
+  content: "\e59a"; }
+
+.fa-file-prescription::before {
+  content: "\f572"; }
+
+.fa-weight-scale::before {
+  content: "\f496"; }
+
+.fa-weight::before {
+  content: "\f496"; }
+
+.fa-user-group::before {
+  content: "\f500"; }
+
+.fa-user-friends::before {
+  content: "\f500"; }
+
+.fa-arrow-up-a-z::before {
+  content: "\f15e"; }
+
+.fa-sort-alpha-up::before {
+  content: "\f15e"; }
+
+.fa-chess-knight::before {
+  content: "\f441"; }
+
+.fa-face-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-wheelchair::before {
+  content: "\f193"; }
+
+.fa-circle-arrow-up::before {
+  content: "\f0aa"; }
+
+.fa-arrow-circle-up::before {
+  content: "\f0aa"; }
+
+.fa-toggle-on::before {
+  content: "\f205"; }
+
+.fa-person-walking::before {
+  content: "\f554"; }
+
+.fa-walking::before {
+  content: "\f554"; }
+
+.fa-l::before {
+  content: "\4c"; }
+
+.fa-fire::before {
+  content: "\f06d"; }
+
+.fa-bed-pulse::before {
+  content: "\f487"; }
+
+.fa-procedures::before {
+  content: "\f487"; }
+
+.fa-shuttle-space::before {
+  content: "\f197"; }
+
+.fa-space-shuttle::before {
+  content: "\f197"; }
+
+.fa-face-laugh::before {
+  content: "\f599"; }
+
+.fa-laugh::before {
+  content: "\f599"; }
+
+.fa-folder-open::before {
+  content: "\f07c"; }
+
+.fa-heart-circle-plus::before {
+  content: "\e500"; }
+
+.fa-code-fork::before {
+  content: "\e13b"; }
+
+.fa-city::before {
+  content: "\f64f"; }
+
+.fa-microphone-lines::before {
+  content: "\f3c9"; }
+
+.fa-microphone-alt::before {
+  content: "\f3c9"; }
+
+.fa-pepper-hot::before {
+  content: "\f816"; }
+
+.fa-unlock::before {
+  content: "\f09c"; }
+
+.fa-colon-sign::before {
+  content: "\e140"; }
+
+.fa-headset::before {
+  content: "\f590"; }
+
+.fa-store-slash::before {
+  content: "\e071"; }
+
+.fa-road-circle-xmark::before {
+  content: "\e566"; }
+
+.fa-user-minus::before {
+  content: "\f503"; }
+
+.fa-mars-stroke-up::before {
+  content: "\f22a"; }
+
+.fa-mars-stroke-v::before {
+  content: "\f22a"; }
+
+.fa-champagne-glasses::before {
+  content: "\f79f"; }
+
+.fa-glass-cheers::before {
+  content: "\f79f"; }
+
+.fa-clipboard::before {
+  content: "\f328"; }
+
+.fa-house-circle-exclamation::before {
+  content: "\e50a"; }
+
+.fa-file-arrow-up::before {
+  content: "\f574"; }
+
+.fa-file-upload::before {
+  content: "\f574"; }
+
+.fa-wifi::before {
+  content: "\f1eb"; }
+
+.fa-wifi-3::before {
+  content: "\f1eb"; }
+
+.fa-wifi-strong::before {
+  content: "\f1eb"; }
+
+.fa-bath::before {
+  content: "\f2cd"; }
+
+.fa-bathtub::before {
+  content: "\f2cd"; }
+
+.fa-underline::before {
+  content: "\f0cd"; }
+
+.fa-user-pen::before {
+  content: "\f4ff"; }
+
+.fa-user-edit::before {
+  content: "\f4ff"; }
+
+.fa-signature::before {
+  content: "\f5b7"; }
+
+.fa-stroopwafel::before {
+  content: "\f551"; }
+
+.fa-bold::before {
+  content: "\f032"; }
+
+.fa-anchor-lock::before {
+  content: "\e4ad"; }
+
+.fa-building-ngo::before {
+  content: "\e4d7"; }
+
+.fa-manat-sign::before {
+  content: "\e1d5"; }
+
+.fa-not-equal::before {
+  content: "\f53e"; }
+
+.fa-border-top-left::before {
+  content: "\f853"; }
+
+.fa-border-style::before {
+  content: "\f853"; }
+
+.fa-map-location-dot::before {
+  content: "\f5a0"; }
+
+.fa-map-marked-alt::before {
+  content: "\f5a0"; }
+
+.fa-jedi::before {
+  content: "\f669"; }
+
+.fa-square-poll-vertical::before {
+  content: "\f681"; }
+
+.fa-poll::before {
+  content: "\f681"; }
+
+.fa-mug-hot::before {
+  content: "\f7b6"; }
+
+.fa-car-battery::before {
+  content: "\f5df"; }
+
+.fa-battery-car::before {
+  content: "\f5df"; }
+
+.fa-gift::before {
+  content: "\f06b"; }
+
+.fa-dice-two::before {
+  content: "\f528"; }
+
+.fa-chess-queen::before {
+  content: "\f445"; }
+
+.fa-glasses::before {
+  content: "\f530"; }
+
+.fa-chess-board::before {
+  content: "\f43c"; }
+
+.fa-building-circle-check::before {
+  content: "\e4d2"; }
+
+.fa-person-chalkboard::before {
+  content: "\e53d"; }
+
+.fa-mars-stroke-right::before {
+  content: "\f22b"; }
+
+.fa-mars-stroke-h::before {
+  content: "\f22b"; }
+
+.fa-hand-back-fist::before {
+  content: "\f255"; }
+
+.fa-hand-rock::before {
+  content: "\f255"; }
+
+.fa-square-caret-up::before {
+  content: "\f151"; }
+
+.fa-caret-square-up::before {
+  content: "\f151"; }
+
+.fa-cloud-showers-water::before {
+  content: "\e4e4"; }
+
+.fa-chart-bar::before {
+  content: "\f080"; }
+
+.fa-bar-chart::before {
+  content: "\f080"; }
+
+.fa-hands-bubbles::before {
+  content: "\e05e"; }
+
+.fa-hands-wash::before {
+  content: "\e05e"; }
+
+.fa-less-than-equal::before {
+  content: "\f537"; }
+
+.fa-train::before {
+  content: "\f238"; }
+
+.fa-eye-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-crow::before {
+  content: "\f520"; }
+
+.fa-sailboat::before {
+  content: "\e445"; }
+
+.fa-window-restore::before {
+  content: "\f2d2"; }
+
+.fa-square-plus::before {
+  content: "\f0fe"; }
+
+.fa-plus-square::before {
+  content: "\f0fe"; }
+
+.fa-torii-gate::before {
+  content: "\f6a1"; }
+
+.fa-frog::before {
+  content: "\f52e"; }
+
+.fa-bucket::before {
+  content: "\e4cf"; }
+
+.fa-image::before {
+  content: "\f03e"; }
+
+.fa-microphone::before {
+  content: "\f130"; }
+
+.fa-cow::before {
+  content: "\f6c8"; }
+
+.fa-caret-up::before {
+  content: "\f0d8"; }
+
+.fa-screwdriver::before {
+  content: "\f54a"; }
+
+.fa-folder-closed::before {
+  content: "\e185"; }
+
+.fa-house-tsunami::before {
+  content: "\e515"; }
+
+.fa-square-nfi::before {
+  content: "\e576"; }
+
+.fa-arrow-up-from-ground-water::before {
+  content: "\e4b5"; }
+
+.fa-martini-glass::before {
+  content: "\f57b"; }
+
+.fa-glass-martini-alt::before {
+  content: "\f57b"; }
+
+.fa-rotate-left::before {
+  content: "\f2ea"; }
+
+.fa-rotate-back::before {
+  content: "\f2ea"; }
+
+.fa-rotate-backward::before {
+  content: "\f2ea"; }
+
+.fa-undo-alt::before {
+  content: "\f2ea"; }
+
+.fa-table-columns::before {
+  content: "\f0db"; }
+
+.fa-columns::before {
+  content: "\f0db"; }
+
+.fa-lemon::before {
+  content: "\f094"; }
+
+.fa-head-side-mask::before {
+  content: "\e063"; }
+
+.fa-handshake::before {
+  content: "\f2b5"; }
+
+.fa-gem::before {
+  content: "\f3a5"; }
+
+.fa-dolly::before {
+  content: "\f472"; }
+
+.fa-dolly-box::before {
+  content: "\f472"; }
+
+.fa-smoking::before {
+  content: "\f48d"; }
+
+.fa-minimize::before {
+  content: "\f78c"; }
+
+.fa-compress-arrows-alt::before {
+  content: "\f78c"; }
+
+.fa-monument::before {
+  content: "\f5a6"; }
+
+.fa-snowplow::before {
+  content: "\f7d2"; }
+
+.fa-angles-right::before {
+  content: "\f101"; }
+
+.fa-angle-double-right::before {
+  content: "\f101"; }
+
+.fa-cannabis::before {
+  content: "\f55f"; }
+
+.fa-circle-play::before {
+  content: "\f144"; }
+
+.fa-play-circle::before {
+  content: "\f144"; }
+
+.fa-tablets::before {
+  content: "\f490"; }
+
+.fa-ethernet::before {
+  content: "\f796"; }
+
+.fa-euro-sign::before {
+  content: "\f153"; }
+
+.fa-eur::before {
+  content: "\f153"; }
+
+.fa-euro::before {
+  content: "\f153"; }
+
+.fa-chair::before {
+  content: "\f6c0"; }
+
+.fa-circle-check::before {
+  content: "\f058"; }
+
+.fa-check-circle::before {
+  content: "\f058"; }
+
+.fa-circle-stop::before {
+  content: "\f28d"; }
+
+.fa-stop-circle::before {
+  content: "\f28d"; }
+
+.fa-compass-drafting::before {
+  content: "\f568"; }
+
+.fa-drafting-compass::before {
+  content: "\f568"; }
+
+.fa-plate-wheat::before {
+  content: "\e55a"; }
+
+.fa-icicles::before {
+  content: "\f7ad"; }
+
+.fa-person-shelter::before {
+  content: "\e54f"; }
+
+.fa-neuter::before {
+  content: "\f22c"; }
+
+.fa-id-badge::before {
+  content: "\f2c1"; }
+
+.fa-marker::before {
+  content: "\f5a1"; }
+
+.fa-face-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-helicopter-symbol::before {
+  content: "\e502"; }
+
+.fa-universal-access::before {
+  content: "\f29a"; }
+
+.fa-circle-chevron-up::before {
+  content: "\f139"; }
+
+.fa-chevron-circle-up::before {
+  content: "\f139"; }
+
+.fa-lari-sign::before {
+  content: "\e1c8"; }
+
+.fa-volcano::before {
+  content: "\f770"; }
+
+.fa-person-walking-dashed-line-arrow-right::before {
+  content: "\e553"; }
+
+.fa-sterling-sign::before {
+  content: "\f154"; }
+
+.fa-gbp::before {
+  content: "\f154"; }
+
+.fa-pound-sign::before {
+  content: "\f154"; }
+
+.fa-viruses::before {
+  content: "\e076"; }
+
+.fa-square-person-confined::before {
+  content: "\e577"; }
+
+.fa-user-tie::before {
+  content: "\f508"; }
+
+.fa-arrow-down-long::before {
+  content: "\f175"; }
+
+.fa-long-arrow-down::before {
+  content: "\f175"; }
+
+.fa-tent-arrow-down-to-line::before {
+  content: "\e57e"; }
+
+.fa-certificate::before {
+  content: "\f0a3"; }
+
+.fa-reply-all::before {
+  content: "\f122"; }
+
+.fa-mail-reply-all::before {
+  content: "\f122"; }
+
+.fa-suitcase::before {
+  content: "\f0f2"; }
+
+.fa-person-skating::before {
+  content: "\f7c5"; }
+
+.fa-skating::before {
+  content: "\f7c5"; }
+
+.fa-filter-circle-dollar::before {
+  content: "\f662"; }
+
+.fa-funnel-dollar::before {
+  content: "\f662"; }
+
+.fa-camera-retro::before {
+  content: "\f083"; }
+
+.fa-circle-arrow-down::before {
+  content: "\f0ab"; }
+
+.fa-arrow-circle-down::before {
+  content: "\f0ab"; }
+
+.fa-file-import::before {
+  content: "\f56f"; }
+
+.fa-arrow-right-to-file::before {
+  content: "\f56f"; }
+
+.fa-square-arrow-up-right::before {
+  content: "\f14c"; }
+
+.fa-external-link-square::before {
+  content: "\f14c"; }
+
+.fa-box-open::before {
+  content: "\f49e"; }
+
+.fa-scroll::before {
+  content: "\f70e"; }
+
+.fa-spa::before {
+  content: "\f5bb"; }
+
+.fa-location-pin-lock::before {
+  content: "\e51f"; }
+
+.fa-pause::before {
+  content: "\f04c"; }
+
+.fa-hill-avalanche::before {
+  content: "\e507"; }
+
+.fa-temperature-empty::before {
+  content: "\f2cb"; }
+
+.fa-temperature-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-empty::before {
+  content: "\f2cb"; }
+
+.fa-bomb::before {
+  content: "\f1e2"; }
+
+.fa-registered::before {
+  content: "\f25d"; }
+
+.fa-address-card::before {
+  content: "\f2bb"; }
+
+.fa-contact-card::before {
+  content: "\f2bb"; }
+
+.fa-vcard::before {
+  content: "\f2bb"; }
+
+.fa-scale-unbalanced-flip::before {
+  content: "\f516"; }
+
+.fa-balance-scale-right::before {
+  content: "\f516"; }
+
+.fa-subscript::before {
+  content: "\f12c"; }
+
+.fa-diamond-turn-right::before {
+  content: "\f5eb"; }
+
+.fa-directions::before {
+  content: "\f5eb"; }
+
+.fa-burst::before {
+  content: "\e4dc"; }
+
+.fa-house-laptop::before {
+  content: "\e066"; }
+
+.fa-laptop-house::before {
+  content: "\e066"; }
+
+.fa-face-tired::before {
+  content: "\f5c8"; }
+
+.fa-tired::before {
+  content: "\f5c8"; }
+
+.fa-money-bills::before {
+  content: "\e1f3"; }
+
+.fa-smog::before {
+  content: "\f75f"; }
+
+.fa-crutch::before {
+  content: "\f7f7"; }
+
+.fa-cloud-arrow-up::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload-alt::before {
+  content: "\f0ee"; }
+
+.fa-palette::before {
+  content: "\f53f"; }
+
+.fa-arrows-turn-right::before {
+  content: "\e4c0"; }
+
+.fa-vest::before {
+  content: "\e085"; }
+
+.fa-ferry::before {
+  content: "\e4ea"; }
+
+.fa-arrows-down-to-people::before {
+  content: "\e4b9"; }
+
+.fa-seedling::before {
+  content: "\f4d8"; }
+
+.fa-sprout::before {
+  content: "\f4d8"; }
+
+.fa-left-right::before {
+  content: "\f337"; }
+
+.fa-arrows-alt-h::before {
+  content: "\f337"; }
+
+.fa-boxes-packing::before {
+  content: "\e4c7"; }
+
+.fa-circle-arrow-left::before {
+  content: "\f0a8"; }
+
+.fa-arrow-circle-left::before {
+  content: "\f0a8"; }
+
+.fa-group-arrows-rotate::before {
+  content: "\e4f6"; }
+
+.fa-bowl-food::before {
+  content: "\e4c6"; }
+
+.fa-candy-cane::before {
+  content: "\f786"; }
+
+.fa-arrow-down-wide-short::before {
+  content: "\f160"; }
+
+.fa-sort-amount-asc::before {
+  content: "\f160"; }
+
+.fa-sort-amount-down::before {
+  content: "\f160"; }
+
+.fa-cloud-bolt::before {
+  content: "\f76c"; }
+
+.fa-thunderstorm::before {
+  content: "\f76c"; }
+
+.fa-text-slash::before {
+  content: "\f87d"; }
+
+.fa-remove-format::before {
+  content: "\f87d"; }
+
+.fa-face-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-file-word::before {
+  content: "\f1c2"; }
+
+.fa-file-powerpoint::before {
+  content: "\f1c4"; }
+
+.fa-arrows-left-right::before {
+  content: "\f07e"; }
+
+.fa-arrows-h::before {
+  content: "\f07e"; }
+
+.fa-house-lock::before {
+  content: "\e510"; }
+
+.fa-cloud-arrow-down::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download-alt::before {
+  content: "\f0ed"; }
+
+.fa-children::before {
+  content: "\e4e1"; }
+
+.fa-chalkboard::before {
+  content: "\f51b"; }
+
+.fa-blackboard::before {
+  content: "\f51b"; }
+
+.fa-user-large-slash::before {
+  content: "\f4fa"; }
+
+.fa-user-alt-slash::before {
+  content: "\f4fa"; }
+
+.fa-envelope-open::before {
+  content: "\f2b6"; }
+
+.fa-handshake-simple-slash::before {
+  content: "\e05f"; }
+
+.fa-handshake-alt-slash::before {
+  content: "\e05f"; }
+
+.fa-mattress-pillow::before {
+  content: "\e525"; }
+
+.fa-guarani-sign::before {
+  content: "\e19a"; }
+
+.fa-arrows-rotate::before {
+  content: "\f021"; }
+
+.fa-refresh::before {
+  content: "\f021"; }
+
+.fa-sync::before {
+  content: "\f021"; }
+
+.fa-fire-extinguisher::before {
+  content: "\f134"; }
+
+.fa-cruzeiro-sign::before {
+  content: "\e152"; }
+
+.fa-greater-than-equal::before {
+  content: "\f532"; }
+
+.fa-shield-halved::before {
+  content: "\f3ed"; }
+
+.fa-shield-alt::before {
+  content: "\f3ed"; }
+
+.fa-book-atlas::before {
+  content: "\f558"; }
+
+.fa-atlas::before {
+  content: "\f558"; }
+
+.fa-virus::before {
+  content: "\e074"; }
+
+.fa-envelope-circle-check::before {
+  content: "\e4e8"; }
+
+.fa-layer-group::before {
+  content: "\f5fd"; }
+
+.fa-arrows-to-dot::before {
+  content: "\e4be"; }
+
+.fa-archway::before {
+  content: "\f557"; }
+
+.fa-heart-circle-check::before {
+  content: "\e4fd"; }
+
+.fa-house-chimney-crack::before {
+  content: "\f6f1"; }
+
+.fa-house-damage::before {
+  content: "\f6f1"; }
+
+.fa-file-zipper::before {
+  content: "\f1c6"; }
+
+.fa-file-archive::before {
+  content: "\f1c6"; }
+
+.fa-square::before {
+  content: "\f0c8"; }
+
+.fa-martini-glass-empty::before {
+  content: "\f000"; }
+
+.fa-glass-martini::before {
+  content: "\f000"; }
+
+.fa-couch::before {
+  content: "\f4b8"; }
+
+.fa-cedi-sign::before {
+  content: "\e0df"; }
+
+.fa-italic::before {
+  content: "\f033"; }
+
+.fa-table-cells-column-lock::before {
+  content: "\e678"; }
+
+.fa-church::before {
+  content: "\f51d"; }
+
+.fa-comments-dollar::before {
+  content: "\f653"; }
+
+.fa-democrat::before {
+  content: "\f747"; }
+
+.fa-z::before {
+  content: "\5a"; }
+
+.fa-person-skiing::before {
+  content: "\f7c9"; }
+
+.fa-skiing::before {
+  content: "\f7c9"; }
+
+.fa-road-lock::before {
+  content: "\e567"; }
+
+.fa-a::before {
+  content: "\41"; }
+
+.fa-temperature-arrow-down::before {
+  content: "\e03f"; }
+
+.fa-temperature-down::before {
+  content: "\e03f"; }
+
+.fa-feather-pointed::before {
+  content: "\f56b"; }
+
+.fa-feather-alt::before {
+  content: "\f56b"; }
+
+.fa-p::before {
+  content: "\50"; }
+
+.fa-snowflake::before {
+  content: "\f2dc"; }
+
+.fa-newspaper::before {
+  content: "\f1ea"; }
+
+.fa-rectangle-ad::before {
+  content: "\f641"; }
+
+.fa-ad::before {
+  content: "\f641"; }
+
+.fa-circle-arrow-right::before {
+  content: "\f0a9"; }
+
+.fa-arrow-circle-right::before {
+  content: "\f0a9"; }
+
+.fa-filter-circle-xmark::before {
+  content: "\e17b"; }
+
+.fa-locust::before {
+  content: "\e520"; }
+
+.fa-sort::before {
+  content: "\f0dc"; }
+
+.fa-unsorted::before {
+  content: "\f0dc"; }
+
+.fa-list-ol::before {
+  content: "\f0cb"; }
+
+.fa-list-1-2::before {
+  content: "\f0cb"; }
+
+.fa-list-numeric::before {
+  content: "\f0cb"; }
+
+.fa-person-dress-burst::before {
+  content: "\e544"; }
+
+.fa-money-check-dollar::before {
+  content: "\f53d"; }
+
+.fa-money-check-alt::before {
+  content: "\f53d"; }
+
+.fa-vector-square::before {
+  content: "\f5cb"; }
+
+.fa-bread-slice::before {
+  content: "\f7ec"; }
+
+.fa-language::before {
+  content: "\f1ab"; }
+
+.fa-face-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-filter::before {
+  content: "\f0b0"; }
+
+.fa-question::before {
+  content: "\3f"; }
+
+.fa-file-signature::before {
+  content: "\f573"; }
+
+.fa-up-down-left-right::before {
+  content: "\f0b2"; }
+
+.fa-arrows-alt::before {
+  content: "\f0b2"; }
+
+.fa-house-chimney-user::before {
+  content: "\e065"; }
+
+.fa-hand-holding-heart::before {
+  content: "\f4be"; }
+
+.fa-puzzle-piece::before {
+  content: "\f12e"; }
+
+.fa-money-check::before {
+  content: "\f53c"; }
+
+.fa-star-half-stroke::before {
+  content: "\f5c0"; }
+
+.fa-star-half-alt::before {
+  content: "\f5c0"; }
+
+.fa-code::before {
+  content: "\f121"; }
+
+.fa-whiskey-glass::before {
+  content: "\f7a0"; }
+
+.fa-glass-whiskey::before {
+  content: "\f7a0"; }
+
+.fa-building-circle-exclamation::before {
+  content: "\e4d3"; }
+
+.fa-magnifying-glass-chart::before {
+  content: "\e522"; }
+
+.fa-arrow-up-right-from-square::before {
+  content: "\f08e"; }
+
+.fa-external-link::before {
+  content: "\f08e"; }
+
+.fa-cubes-stacked::before {
+  content: "\e4e6"; }
+
+.fa-won-sign::before {
+  content: "\f159"; }
+
+.fa-krw::before {
+  content: "\f159"; }
+
+.fa-won::before {
+  content: "\f159"; }
+
+.fa-virus-covid::before {
+  content: "\e4a8"; }
+
+.fa-austral-sign::before {
+  content: "\e0a9"; }
+
+.fa-f::before {
+  content: "\46"; }
+
+.fa-leaf::before {
+  content: "\f06c"; }
+
+.fa-road::before {
+  content: "\f018"; }
+
+.fa-taxi::before {
+  content: "\f1ba"; }
+
+.fa-cab::before {
+  content: "\f1ba"; }
+
+.fa-person-circle-plus::before {
+  content: "\e541"; }
+
+.fa-chart-pie::before {
+  content: "\f200"; }
+
+.fa-pie-chart::before {
+  content: "\f200"; }
+
+.fa-bolt-lightning::before {
+  content: "\e0b7"; }
+
+.fa-sack-xmark::before {
+  content: "\e56a"; }
+
+.fa-file-excel::before {
+  content: "\f1c3"; }
+
+.fa-file-contract::before {
+  content: "\f56c"; }
+
+.fa-fish-fins::before {
+  content: "\e4f2"; }
+
+.fa-building-flag::before {
+  content: "\e4d5"; }
+
+.fa-face-grin-beam::before {
+  content: "\f582"; }
+
+.fa-grin-beam::before {
+  content: "\f582"; }
+
+.fa-object-ungroup::before {
+  content: "\f248"; }
+
+.fa-poop::before {
+  content: "\f619"; }
+
+.fa-location-pin::before {
+  content: "\f041"; }
+
+.fa-map-marker::before {
+  content: "\f041"; }
+
+.fa-kaaba::before {
+  content: "\f66b"; }
+
+.fa-toilet-paper::before {
+  content: "\f71e"; }
+
+.fa-helmet-safety::before {
+  content: "\f807"; }
+
+.fa-hard-hat::before {
+  content: "\f807"; }
+
+.fa-hat-hard::before {
+  content: "\f807"; }
+
+.fa-eject::before {
+  content: "\f052"; }
+
+.fa-circle-right::before {
+  content: "\f35a"; }
+
+.fa-arrow-alt-circle-right::before {
+  content: "\f35a"; }
+
+.fa-plane-circle-check::before {
+  content: "\e555"; }
+
+.fa-face-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-meh-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-object-group::before {
+  content: "\f247"; }
+
+.fa-chart-line::before {
+  content: "\f201"; }
+
+.fa-line-chart::before {
+  content: "\f201"; }
+
+.fa-mask-ventilator::before {
+  content: "\e524"; }
+
+.fa-arrow-right::before {
+  content: "\f061"; }
+
+.fa-signs-post::before {
+  content: "\f277"; }
+
+.fa-map-signs::before {
+  content: "\f277"; }
+
+.fa-cash-register::before {
+  content: "\f788"; }
+
+.fa-person-circle-question::before {
+  content: "\e542"; }
+
+.fa-h::before {
+  content: "\48"; }
+
+.fa-tarp::before {
+  content: "\e57b"; }
+
+.fa-screwdriver-wrench::before {
+  content: "\f7d9"; }
+
+.fa-tools::before {
+  content: "\f7d9"; }
+
+.fa-arrows-to-eye::before {
+  content: "\e4bf"; }
+
+.fa-plug-circle-bolt::before {
+  content: "\e55b"; }
+
+.fa-heart::before {
+  content: "\f004"; }
+
+.fa-mars-and-venus::before {
+  content: "\f224"; }
+
+.fa-house-user::before {
+  content: "\e1b0"; }
+
+.fa-home-user::before {
+  content: "\e1b0"; }
+
+.fa-dumpster-fire::before {
+  content: "\f794"; }
+
+.fa-house-crack::before {
+  content: "\e3b1"; }
+
+.fa-martini-glass-citrus::before {
+  content: "\f561"; }
+
+.fa-cocktail::before {
+  content: "\f561"; }
+
+.fa-face-surprise::before {
+  content: "\f5c2"; }
+
+.fa-surprise::before {
+  content: "\f5c2"; }
+
+.fa-bottle-water::before {
+  content: "\e4c5"; }
+
+.fa-circle-pause::before {
+  content: "\f28b"; }
+
+.fa-pause-circle::before {
+  content: "\f28b"; }
+
+.fa-toilet-paper-slash::before {
+  content: "\e072"; }
+
+.fa-apple-whole::before {
+  content: "\f5d1"; }
+
+.fa-apple-alt::before {
+  content: "\f5d1"; }
+
+.fa-kitchen-set::before {
+  content: "\e51a"; }
+
+.fa-r::before {
+  content: "\52"; }
+
+.fa-temperature-quarter::before {
+  content: "\f2ca"; }
+
+.fa-temperature-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-quarter::before {
+  content: "\f2ca"; }
+
+.fa-cube::before {
+  content: "\f1b2"; }
+
+.fa-bitcoin-sign::before {
+  content: "\e0b4"; }
+
+.fa-shield-dog::before {
+  content: "\e573"; }
+
+.fa-solar-panel::before {
+  content: "\f5ba"; }
+
+.fa-lock-open::before {
+  content: "\f3c1"; }
+
+.fa-elevator::before {
+  content: "\e16d"; }
+
+.fa-money-bill-transfer::before {
+  content: "\e528"; }
+
+.fa-money-bill-trend-up::before {
+  content: "\e529"; }
+
+.fa-house-flood-water-circle-arrow-right::before {
+  content: "\e50f"; }
+
+.fa-square-poll-horizontal::before {
+  content: "\f682"; }
+
+.fa-poll-h::before {
+  content: "\f682"; }
+
+.fa-circle::before {
+  content: "\f111"; }
+
+.fa-backward-fast::before {
+  content: "\f049"; }
+
+.fa-fast-backward::before {
+  content: "\f049"; }
+
+.fa-recycle::before {
+  content: "\f1b8"; }
+
+.fa-user-astronaut::before {
+  content: "\f4fb"; }
+
+.fa-plane-slash::before {
+  content: "\e069"; }
+
+.fa-trademark::before {
+  content: "\f25c"; }
+
+.fa-basketball::before {
+  content: "\f434"; }
+
+.fa-basketball-ball::before {
+  content: "\f434"; }
+
+.fa-satellite-dish::before {
+  content: "\f7c0"; }
+
+.fa-circle-up::before {
+  content: "\f35b"; }
+
+.fa-arrow-alt-circle-up::before {
+  content: "\f35b"; }
+
+.fa-mobile-screen-button::before {
+  content: "\f3cd"; }
+
+.fa-mobile-alt::before {
+  content: "\f3cd"; }
+
+.fa-volume-high::before {
+  content: "\f028"; }
+
+.fa-volume-up::before {
+  content: "\f028"; }
+
+.fa-users-rays::before {
+  content: "\e593"; }
+
+.fa-wallet::before {
+  content: "\f555"; }
+
+.fa-clipboard-check::before {
+  content: "\f46c"; }
+
+.fa-file-audio::before {
+  content: "\f1c7"; }
+
+.fa-burger::before {
+  content: "\f805"; }
+
+.fa-hamburger::before {
+  content: "\f805"; }
+
+.fa-wrench::before {
+  content: "\f0ad"; }
+
+.fa-bugs::before {
+  content: "\e4d0"; }
+
+.fa-rupee-sign::before {
+  content: "\f156"; }
+
+.fa-rupee::before {
+  content: "\f156"; }
+
+.fa-file-image::before {
+  content: "\f1c5"; }
+
+.fa-circle-question::before {
+  content: "\f059"; }
+
+.fa-question-circle::before {
+  content: "\f059"; }
+
+.fa-plane-departure::before {
+  content: "\f5b0"; }
+
+.fa-handshake-slash::before {
+  content: "\e060"; }
+
+.fa-book-bookmark::before {
+  content: "\e0bb"; }
+
+.fa-code-branch::before {
+  content: "\f126"; }
+
+.fa-hat-cowboy::before {
+  content: "\f8c0"; }
+
+.fa-bridge::before {
+  content: "\e4c8"; }
+
+.fa-phone-flip::before {
+  content: "\f879"; }
+
+.fa-phone-alt::before {
+  content: "\f879"; }
+
+.fa-truck-front::before {
+  content: "\e2b7"; }
+
+.fa-cat::before {
+  content: "\f6be"; }
+
+.fa-anchor-circle-exclamation::before {
+  content: "\e4ab"; }
+
+.fa-truck-field::before {
+  content: "\e58d"; }
+
+.fa-route::before {
+  content: "\f4d7"; }
+
+.fa-clipboard-question::before {
+  content: "\e4e3"; }
+
+.fa-panorama::before {
+  content: "\e209"; }
+
+.fa-comment-medical::before {
+  content: "\f7f5"; }
+
+.fa-teeth-open::before {
+  content: "\f62f"; }
+
+.fa-file-circle-minus::before {
+  content: "\e4ed"; }
+
+.fa-tags::before {
+  content: "\f02c"; }
+
+.fa-wine-glass::before {
+  content: "\f4e3"; }
+
+.fa-forward-fast::before {
+  content: "\f050"; }
+
+.fa-fast-forward::before {
+  content: "\f050"; }
+
+.fa-face-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-square-parking::before {
+  content: "\f540"; }
+
+.fa-parking::before {
+  content: "\f540"; }
+
+.fa-house-signal::before {
+  content: "\e012"; }
+
+.fa-bars-progress::before {
+  content: "\f828"; }
+
+.fa-tasks-alt::before {
+  content: "\f828"; }
+
+.fa-faucet-drip::before {
+  content: "\e006"; }
+
+.fa-cart-flatbed::before {
+  content: "\f474"; }
+
+.fa-dolly-flatbed::before {
+  content: "\f474"; }
+
+.fa-ban-smoking::before {
+  content: "\f54d"; }
+
+.fa-smoking-ban::before {
+  content: "\f54d"; }
+
+.fa-terminal::before {
+  content: "\f120"; }
+
+.fa-mobile-button::before {
+  content: "\f10b"; }
+
+.fa-house-medical-flag::before {
+  content: "\e514"; }
+
+.fa-basket-shopping::before {
+  content: "\f291"; }
+
+.fa-shopping-basket::before {
+  content: "\f291"; }
+
+.fa-tape::before {
+  content: "\f4db"; }
+
+.fa-bus-simple::before {
+  content: "\f55e"; }
+
+.fa-bus-alt::before {
+  content: "\f55e"; }
+
+.fa-eye::before {
+  content: "\f06e"; }
+
+.fa-face-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-audio-description::before {
+  content: "\f29e"; }
+
+.fa-person-military-to-person::before {
+  content: "\e54c"; }
+
+.fa-file-shield::before {
+  content: "\e4f0"; }
+
+.fa-user-slash::before {
+  content: "\f506"; }
+
+.fa-pen::before {
+  content: "\f304"; }
+
+.fa-tower-observation::before {
+  content: "\e586"; }
+
+.fa-file-code::before {
+  content: "\f1c9"; }
+
+.fa-signal::before {
+  content: "\f012"; }
+
+.fa-signal-5::before {
+  content: "\f012"; }
+
+.fa-signal-perfect::before {
+  content: "\f012"; }
+
+.fa-bus::before {
+  content: "\f207"; }
+
+.fa-heart-circle-xmark::before {
+  content: "\e501"; }
+
+.fa-house-chimney::before {
+  content: "\e3af"; }
+
+.fa-home-lg::before {
+  content: "\e3af"; }
+
+.fa-window-maximize::before {
+  content: "\f2d0"; }
+
+.fa-face-frown::before {
+  content: "\f119"; }
+
+.fa-frown::before {
+  content: "\f119"; }
+
+.fa-prescription::before {
+  content: "\f5b1"; }
+
+.fa-shop::before {
+  content: "\f54f"; }
+
+.fa-store-alt::before {
+  content: "\f54f"; }
+
+.fa-floppy-disk::before {
+  content: "\f0c7"; }
+
+.fa-save::before {
+  content: "\f0c7"; }
+
+.fa-vihara::before {
+  content: "\f6a7"; }
+
+.fa-scale-unbalanced::before {
+  content: "\f515"; }
+
+.fa-balance-scale-left::before {
+  content: "\f515"; }
+
+.fa-sort-up::before {
+  content: "\f0de"; }
+
+.fa-sort-asc::before {
+  content: "\f0de"; }
+
+.fa-comment-dots::before {
+  content: "\f4ad"; }
+
+.fa-commenting::before {
+  content: "\f4ad"; }
+
+.fa-plant-wilt::before {
+  content: "\e5aa"; }
+
+.fa-diamond::before {
+  content: "\f219"; }
+
+.fa-face-grin-squint::before {
+  content: "\f585"; }
+
+.fa-grin-squint::before {
+  content: "\f585"; }
+
+.fa-hand-holding-dollar::before {
+  content: "\f4c0"; }
+
+.fa-hand-holding-usd::before {
+  content: "\f4c0"; }
+
+.fa-bacterium::before {
+  content: "\e05a"; }
+
+.fa-hand-pointer::before {
+  content: "\f25a"; }
+
+.fa-drum-steelpan::before {
+  content: "\f56a"; }
+
+.fa-hand-scissors::before {
+  content: "\f257"; }
+
+.fa-hands-praying::before {
+  content: "\f684"; }
+
+.fa-praying-hands::before {
+  content: "\f684"; }
+
+.fa-arrow-rotate-right::before {
+  content: "\f01e"; }
+
+.fa-arrow-right-rotate::before {
+  content: "\f01e"; }
+
+.fa-arrow-rotate-forward::before {
+  content: "\f01e"; }
+
+.fa-redo::before {
+  content: "\f01e"; }
+
+.fa-biohazard::before {
+  content: "\f780"; }
+
+.fa-location-crosshairs::before {
+  content: "\f601"; }
+
+.fa-location::before {
+  content: "\f601"; }
+
+.fa-mars-double::before {
+  content: "\f227"; }
+
+.fa-child-dress::before {
+  content: "\e59c"; }
+
+.fa-users-between-lines::before {
+  content: "\e591"; }
+
+.fa-lungs-virus::before {
+  content: "\e067"; }
+
+.fa-face-grin-tears::before {
+  content: "\f588"; }
+
+.fa-grin-tears::before {
+  content: "\f588"; }
+
+.fa-phone::before {
+  content: "\f095"; }
+
+.fa-calendar-xmark::before {
+  content: "\f273"; }
+
+.fa-calendar-times::before {
+  content: "\f273"; }
+
+.fa-child-reaching::before {
+  content: "\e59d"; }
+
+.fa-head-side-virus::before {
+  content: "\e064"; }
+
+.fa-user-gear::before {
+  content: "\f4fe"; }
+
+.fa-user-cog::before {
+  content: "\f4fe"; }
+
+.fa-arrow-up-1-9::before {
+  content: "\f163"; }
+
+.fa-sort-numeric-up::before {
+  content: "\f163"; }
+
+.fa-door-closed::before {
+  content: "\f52a"; }
+
+.fa-shield-virus::before {
+  content: "\e06c"; }
+
+.fa-dice-six::before {
+  content: "\f526"; }
+
+.fa-mosquito-net::before {
+  content: "\e52c"; }
+
+.fa-bridge-water::before {
+  content: "\e4ce"; }
+
+.fa-person-booth::before {
+  content: "\f756"; }
+
+.fa-text-width::before {
+  content: "\f035"; }
+
+.fa-hat-wizard::before {
+  content: "\f6e8"; }
+
+.fa-pen-fancy::before {
+  content: "\f5ac"; }
+
+.fa-person-digging::before {
+  content: "\f85e"; }
+
+.fa-digging::before {
+  content: "\f85e"; }
+
+.fa-trash::before {
+  content: "\f1f8"; }
+
+.fa-gauge-simple::before {
+  content: "\f629"; }
+
+.fa-gauge-simple-med::before {
+  content: "\f629"; }
+
+.fa-tachometer-average::before {
+  content: "\f629"; }
+
+.fa-book-medical::before {
+  content: "\f7e6"; }
+
+.fa-poo::before {
+  content: "\f2fe"; }
+
+.fa-quote-right::before {
+  content: "\f10e"; }
+
+.fa-quote-right-alt::before {
+  content: "\f10e"; }
+
+.fa-shirt::before {
+  content: "\f553"; }
+
+.fa-t-shirt::before {
+  content: "\f553"; }
+
+.fa-tshirt::before {
+  content: "\f553"; }
+
+.fa-cubes::before {
+  content: "\f1b3"; }
+
+.fa-divide::before {
+  content: "\f529"; }
+
+.fa-tenge-sign::before {
+  content: "\f7d7"; }
+
+.fa-tenge::before {
+  content: "\f7d7"; }
+
+.fa-headphones::before {
+  content: "\f025"; }
+
+.fa-hands-holding::before {
+  content: "\f4c2"; }
+
+.fa-hands-clapping::before {
+  content: "\e1a8"; }
+
+.fa-republican::before {
+  content: "\f75e"; }
+
+.fa-arrow-left::before {
+  content: "\f060"; }
+
+.fa-person-circle-xmark::before {
+  content: "\e543"; }
+
+.fa-ruler::before {
+  content: "\f545"; }
+
+.fa-align-left::before {
+  content: "\f036"; }
+
+.fa-dice-d6::before {
+  content: "\f6d1"; }
+
+.fa-restroom::before {
+  content: "\f7bd"; }
+
+.fa-j::before {
+  content: "\4a"; }
+
+.fa-users-viewfinder::before {
+  content: "\e595"; }
+
+.fa-file-video::before {
+  content: "\f1c8"; }
+
+.fa-up-right-from-square::before {
+  content: "\f35d"; }
+
+.fa-external-link-alt::before {
+  content: "\f35d"; }
+
+.fa-table-cells::before {
+  content: "\f00a"; }
+
+.fa-th::before {
+  content: "\f00a"; }
+
+.fa-file-pdf::before {
+  content: "\f1c1"; }
+
+.fa-book-bible::before {
+  content: "\f647"; }
+
+.fa-bible::before {
+  content: "\f647"; }
+
+.fa-o::before {
+  content: "\4f"; }
+
+.fa-suitcase-medical::before {
+  content: "\f0fa"; }
+
+.fa-medkit::before {
+  content: "\f0fa"; }
+
+.fa-user-secret::before {
+  content: "\f21b"; }
+
+.fa-otter::before {
+  content: "\f700"; }
+
+.fa-person-dress::before {
+  content: "\f182"; }
+
+.fa-female::before {
+  content: "\f182"; }
+
+.fa-comment-dollar::before {
+  content: "\f651"; }
+
+.fa-business-time::before {
+  content: "\f64a"; }
+
+.fa-briefcase-clock::before {
+  content: "\f64a"; }
+
+.fa-table-cells-large::before {
+  content: "\f009"; }
+
+.fa-th-large::before {
+  content: "\f009"; }
+
+.fa-book-tanakh::before {
+  content: "\f827"; }
+
+.fa-tanakh::before {
+  content: "\f827"; }
+
+.fa-phone-volume::before {
+  content: "\f2a0"; }
+
+.fa-volume-control-phone::before {
+  content: "\f2a0"; }
+
+.fa-hat-cowboy-side::before {
+  content: "\f8c1"; }
+
+.fa-clipboard-user::before {
+  content: "\f7f3"; }
+
+.fa-child::before {
+  content: "\f1ae"; }
+
+.fa-lira-sign::before {
+  content: "\f195"; }
+
+.fa-satellite::before {
+  content: "\f7bf"; }
+
+.fa-plane-lock::before {
+  content: "\e558"; }
+
+.fa-tag::before {
+  content: "\f02b"; }
+
+.fa-comment::before {
+  content: "\f075"; }
+
+.fa-cake-candles::before {
+  content: "\f1fd"; }
+
+.fa-birthday-cake::before {
+  content: "\f1fd"; }
+
+.fa-cake::before {
+  content: "\f1fd"; }
+
+.fa-envelope::before {
+  content: "\f0e0"; }
+
+.fa-angles-up::before {
+  content: "\f102"; }
+
+.fa-angle-double-up::before {
+  content: "\f102"; }
+
+.fa-paperclip::before {
+  content: "\f0c6"; }
+
+.fa-arrow-right-to-city::before {
+  content: "\e4b3"; }
+
+.fa-ribbon::before {
+  content: "\f4d6"; }
+
+.fa-lungs::before {
+  content: "\f604"; }
+
+.fa-arrow-up-9-1::before {
+  content: "\f887"; }
+
+.fa-sort-numeric-up-alt::before {
+  content: "\f887"; }
+
+.fa-litecoin-sign::before {
+  content: "\e1d3"; }
+
+.fa-border-none::before {
+  content: "\f850"; }
+
+.fa-circle-nodes::before {
+  content: "\e4e2"; }
+
+.fa-parachute-box::before {
+  content: "\f4cd"; }
+
+.fa-indent::before {
+  content: "\f03c"; }
+
+.fa-truck-field-un::before {
+  content: "\e58e"; }
+
+.fa-hourglass::before {
+  content: "\f254"; }
+
+.fa-hourglass-empty::before {
+  content: "\f254"; }
+
+.fa-mountain::before {
+  content: "\f6fc"; }
+
+.fa-user-doctor::before {
+  content: "\f0f0"; }
+
+.fa-user-md::before {
+  content: "\f0f0"; }
+
+.fa-circle-info::before {
+  content: "\f05a"; }
+
+.fa-info-circle::before {
+  content: "\f05a"; }
+
+.fa-cloud-meatball::before {
+  content: "\f73b"; }
+
+.fa-camera::before {
+  content: "\f030"; }
+
+.fa-camera-alt::before {
+  content: "\f030"; }
+
+.fa-square-virus::before {
+  content: "\e578"; }
+
+.fa-meteor::before {
+  content: "\f753"; }
+
+.fa-car-on::before {
+  content: "\e4dd"; }
+
+.fa-sleigh::before {
+  content: "\f7cc"; }
+
+.fa-arrow-down-1-9::before {
+  content: "\f162"; }
+
+.fa-sort-numeric-asc::before {
+  content: "\f162"; }
+
+.fa-sort-numeric-down::before {
+  content: "\f162"; }
+
+.fa-hand-holding-droplet::before {
+  content: "\f4c1"; }
+
+.fa-hand-holding-water::before {
+  content: "\f4c1"; }
+
+.fa-water::before {
+  content: "\f773"; }
+
+.fa-calendar-check::before {
+  content: "\f274"; }
+
+.fa-braille::before {
+  content: "\f2a1"; }
+
+.fa-prescription-bottle-medical::before {
+  content: "\f486"; }
+
+.fa-prescription-bottle-alt::before {
+  content: "\f486"; }
+
+.fa-landmark::before {
+  content: "\f66f"; }
+
+.fa-truck::before {
+  content: "\f0d1"; }
+
+.fa-crosshairs::before {
+  content: "\f05b"; }
+
+.fa-person-cane::before {
+  content: "\e53c"; }
+
+.fa-tent::before {
+  content: "\e57d"; }
+
+.fa-vest-patches::before {
+  content: "\e086"; }
+
+.fa-check-double::before {
+  content: "\f560"; }
+
+.fa-arrow-down-a-z::before {
+  content: "\f15d"; }
+
+.fa-sort-alpha-asc::before {
+  content: "\f15d"; }
+
+.fa-sort-alpha-down::before {
+  content: "\f15d"; }
+
+.fa-money-bill-wheat::before {
+  content: "\e52a"; }
+
+.fa-cookie::before {
+  content: "\f563"; }
+
+.fa-arrow-rotate-left::before {
+  content: "\f0e2"; }
+
+.fa-arrow-left-rotate::before {
+  content: "\f0e2"; }
+
+.fa-arrow-rotate-back::before {
+  content: "\f0e2"; }
+
+.fa-arrow-rotate-backward::before {
+  content: "\f0e2"; }
+
+.fa-undo::before {
+  content: "\f0e2"; }
+
+.fa-hard-drive::before {
+  content: "\f0a0"; }
+
+.fa-hdd::before {
+  content: "\f0a0"; }
+
+.fa-face-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-dumbbell::before {
+  content: "\f44b"; }
+
+.fa-rectangle-list::before {
+  content: "\f022"; }
+
+.fa-list-alt::before {
+  content: "\f022"; }
+
+.fa-tarp-droplet::before {
+  content: "\e57c"; }
+
+.fa-house-medical-circle-check::before {
+  content: "\e511"; }
+
+.fa-person-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-calendar-plus::before {
+  content: "\f271"; }
+
+.fa-plane-arrival::before {
+  content: "\f5af"; }
+
+.fa-circle-left::before {
+  content: "\f359"; }
+
+.fa-arrow-alt-circle-left::before {
+  content: "\f359"; }
+
+.fa-train-subway::before {
+  content: "\f239"; }
+
+.fa-subway::before {
+  content: "\f239"; }
+
+.fa-chart-gantt::before {
+  content: "\e0e4"; }
+
+.fa-indian-rupee-sign::before {
+  content: "\e1bc"; }
+
+.fa-indian-rupee::before {
+  content: "\e1bc"; }
+
+.fa-inr::before {
+  content: "\e1bc"; }
+
+.fa-crop-simple::before {
+  content: "\f565"; }
+
+.fa-crop-alt::before {
+  content: "\f565"; }
+
+.fa-money-bill-1::before {
+  content: "\f3d1"; }
+
+.fa-money-bill-alt::before {
+  content: "\f3d1"; }
+
+.fa-left-long::before {
+  content: "\f30a"; }
+
+.fa-long-arrow-alt-left::before {
+  content: "\f30a"; }
+
+.fa-dna::before {
+  content: "\f471"; }
+
+.fa-virus-slash::before {
+  content: "\e075"; }
+
+.fa-minus::before {
+  content: "\f068"; }
+
+.fa-subtract::before {
+  content: "\f068"; }
+
+.fa-chess::before {
+  content: "\f439"; }
+
+.fa-arrow-left-long::before {
+  content: "\f177"; }
+
+.fa-long-arrow-left::before {
+  content: "\f177"; }
+
+.fa-plug-circle-check::before {
+  content: "\e55c"; }
+
+.fa-street-view::before {
+  content: "\f21d"; }
+
+.fa-franc-sign::before {
+  content: "\e18f"; }
+
+.fa-volume-off::before {
+  content: "\f026"; }
+
+.fa-hands-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-hands-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-gear::before {
+  content: "\f013"; }
+
+.fa-cog::before {
+  content: "\f013"; }
+
+.fa-droplet-slash::before {
+  content: "\f5c7"; }
+
+.fa-tint-slash::before {
+  content: "\f5c7"; }
+
+.fa-mosque::before {
+  content: "\f678"; }
+
+.fa-mosquito::before {
+  content: "\e52b"; }
+
+.fa-star-of-david::before {
+  content: "\f69a"; }
+
+.fa-person-military-rifle::before {
+  content: "\e54b"; }
+
+.fa-cart-shopping::before {
+  content: "\f07a"; }
+
+.fa-shopping-cart::before {
+  content: "\f07a"; }
+
+.fa-vials::before {
+  content: "\f493"; }
+
+.fa-plug-circle-plus::before {
+  content: "\e55f"; }
+
+.fa-place-of-worship::before {
+  content: "\f67f"; }
+
+.fa-grip-vertical::before {
+  content: "\f58e"; }
+
+.fa-arrow-turn-up::before {
+  content: "\f148"; }
+
+.fa-level-up::before {
+  content: "\f148"; }
+
+.fa-u::before {
+  content: "\55"; }
+
+.fa-square-root-variable::before {
+  content: "\f698"; }
+
+.fa-square-root-alt::before {
+  content: "\f698"; }
+
+.fa-clock::before {
+  content: "\f017"; }
+
+.fa-clock-four::before {
+  content: "\f017"; }
+
+.fa-backward-step::before {
+  content: "\f048"; }
+
+.fa-step-backward::before {
+  content: "\f048"; }
+
+.fa-pallet::before {
+  content: "\f482"; }
+
+.fa-faucet::before {
+  content: "\e005"; }
+
+.fa-baseball-bat-ball::before {
+  content: "\f432"; }
+
+.fa-s::before {
+  content: "\53"; }
+
+.fa-timeline::before {
+  content: "\e29c"; }
+
+.fa-keyboard::before {
+  content: "\f11c"; }
+
+.fa-caret-down::before {
+  content: "\f0d7"; }
+
+.fa-house-chimney-medical::before {
+  content: "\f7f2"; }
+
+.fa-clinic-medical::before {
+  content: "\f7f2"; }
+
+.fa-temperature-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-temperature-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-mobile-screen::before {
+  content: "\f3cf"; }
+
+.fa-mobile-android-alt::before {
+  content: "\f3cf"; }
+
+.fa-plane-up::before {
+  content: "\e22d"; }
+
+.fa-piggy-bank::before {
+  content: "\f4d3"; }
+
+.fa-battery-half::before {
+  content: "\f242"; }
+
+.fa-battery-3::before {
+  content: "\f242"; }
+
+.fa-mountain-city::before {
+  content: "\e52e"; }
+
+.fa-coins::before {
+  content: "\f51e"; }
+
+.fa-khanda::before {
+  content: "\f66d"; }
+
+.fa-sliders::before {
+  content: "\f1de"; }
+
+.fa-sliders-h::before {
+  content: "\f1de"; }
+
+.fa-folder-tree::before {
+  content: "\f802"; }
+
+.fa-network-wired::before {
+  content: "\f6ff"; }
+
+.fa-map-pin::before {
+  content: "\f276"; }
+
+.fa-hamsa::before {
+  content: "\f665"; }
+
+.fa-cent-sign::before {
+  content: "\e3f5"; }
+
+.fa-flask::before {
+  content: "\f0c3"; }
+
+.fa-person-pregnant::before {
+  content: "\e31e"; }
+
+.fa-wand-sparkles::before {
+  content: "\f72b"; }
+
+.fa-ellipsis-vertical::before {
+  content: "\f142"; }
+
+.fa-ellipsis-v::before {
+  content: "\f142"; }
+
+.fa-ticket::before {
+  content: "\f145"; }
+
+.fa-power-off::before {
+  content: "\f011"; }
+
+.fa-right-long::before {
+  content: "\f30b"; }
+
+.fa-long-arrow-alt-right::before {
+  content: "\f30b"; }
+
+.fa-flag-usa::before {
+  content: "\f74d"; }
+
+.fa-laptop-file::before {
+  content: "\e51d"; }
+
+.fa-tty::before {
+  content: "\f1e4"; }
+
+.fa-teletype::before {
+  content: "\f1e4"; }
+
+.fa-diagram-next::before {
+  content: "\e476"; }
+
+.fa-person-rifle::before {
+  content: "\e54e"; }
+
+.fa-house-medical-circle-exclamation::before {
+  content: "\e512"; }
+
+.fa-closed-captioning::before {
+  content: "\f20a"; }
+
+.fa-person-hiking::before {
+  content: "\f6ec"; }
+
+.fa-hiking::before {
+  content: "\f6ec"; }
+
+.fa-venus-double::before {
+  content: "\f226"; }
+
+.fa-images::before {
+  content: "\f302"; }
+
+.fa-calculator::before {
+  content: "\f1ec"; }
+
+.fa-people-pulling::before {
+  content: "\e535"; }
+
+.fa-n::before {
+  content: "\4e"; }
+
+.fa-cable-car::before {
+  content: "\f7da"; }
+
+.fa-tram::before {
+  content: "\f7da"; }
+
+.fa-cloud-rain::before {
+  content: "\f73d"; }
+
+.fa-building-circle-xmark::before {
+  content: "\e4d4"; }
+
+.fa-ship::before {
+  content: "\f21a"; }
+
+.fa-arrows-down-to-line::before {
+  content: "\e4b8"; }
+
+.fa-download::before {
+  content: "\f019"; }
+
+.fa-face-grin::before {
+  content: "\f580"; }
+
+.fa-grin::before {
+  content: "\f580"; }
+
+.fa-delete-left::before {
+  content: "\f55a"; }
+
+.fa-backspace::before {
+  content: "\f55a"; }
+
+.fa-eye-dropper::before {
+  content: "\f1fb"; }
+
+.fa-eye-dropper-empty::before {
+  content: "\f1fb"; }
+
+.fa-eyedropper::before {
+  content: "\f1fb"; }
+
+.fa-file-circle-check::before {
+  content: "\e5a0"; }
+
+.fa-forward::before {
+  content: "\f04e"; }
+
+.fa-mobile::before {
+  content: "\f3ce"; }
+
+.fa-mobile-android::before {
+  content: "\f3ce"; }
+
+.fa-mobile-phone::before {
+  content: "\f3ce"; }
+
+.fa-face-meh::before {
+  content: "\f11a"; }
+
+.fa-meh::before {
+  content: "\f11a"; }
+
+.fa-align-center::before {
+  content: "\f037"; }
+
+.fa-book-skull::before {
+  content: "\f6b7"; }
+
+.fa-book-dead::before {
+  content: "\f6b7"; }
+
+.fa-id-card::before {
+  content: "\f2c2"; }
+
+.fa-drivers-license::before {
+  content: "\f2c2"; }
+
+.fa-outdent::before {
+  content: "\f03b"; }
+
+.fa-dedent::before {
+  content: "\f03b"; }
+
+.fa-heart-circle-exclamation::before {
+  content: "\e4fe"; }
+
+.fa-house::before {
+  content: "\f015"; }
+
+.fa-home::before {
+  content: "\f015"; }
+
+.fa-home-alt::before {
+  content: "\f015"; }
+
+.fa-home-lg-alt::before {
+  content: "\f015"; }
+
+.fa-calendar-week::before {
+  content: "\f784"; }
+
+.fa-laptop-medical::before {
+  content: "\f812"; }
+
+.fa-b::before {
+  content: "\42"; }
+
+.fa-file-medical::before {
+  content: "\f477"; }
+
+.fa-dice-one::before {
+  content: "\f525"; }
+
+.fa-kiwi-bird::before {
+  content: "\f535"; }
+
+.fa-arrow-right-arrow-left::before {
+  content: "\f0ec"; }
+
+.fa-exchange::before {
+  content: "\f0ec"; }
+
+.fa-rotate-right::before {
+  content: "\f2f9"; }
+
+.fa-redo-alt::before {
+  content: "\f2f9"; }
+
+.fa-rotate-forward::before {
+  content: "\f2f9"; }
+
+.fa-utensils::before {
+  content: "\f2e7"; }
+
+.fa-cutlery::before {
+  content: "\f2e7"; }
+
+.fa-arrow-up-wide-short::before {
+  content: "\f161"; }
+
+.fa-sort-amount-up::before {
+  content: "\f161"; }
+
+.fa-mill-sign::before {
+  content: "\e1ed"; }
+
+.fa-bowl-rice::before {
+  content: "\e2eb"; }
+
+.fa-skull::before {
+  content: "\f54c"; }
+
+.fa-tower-broadcast::before {
+  content: "\f519"; }
+
+.fa-broadcast-tower::before {
+  content: "\f519"; }
+
+.fa-truck-pickup::before {
+  content: "\f63c"; }
+
+.fa-up-long::before {
+  content: "\f30c"; }
+
+.fa-long-arrow-alt-up::before {
+  content: "\f30c"; }
+
+.fa-stop::before {
+  content: "\f04d"; }
+
+.fa-code-merge::before {
+  content: "\f387"; }
+
+.fa-upload::before {
+  content: "\f093"; }
+
+.fa-hurricane::before {
+  content: "\f751"; }
+
+.fa-mound::before {
+  content: "\e52d"; }
+
+.fa-toilet-portable::before {
+  content: "\e583"; }
+
+.fa-compact-disc::before {
+  content: "\f51f"; }
+
+.fa-file-arrow-down::before {
+  content: "\f56d"; }
+
+.fa-file-download::before {
+  content: "\f56d"; }
+
+.fa-caravan::before {
+  content: "\f8ff"; }
+
+.fa-shield-cat::before {
+  content: "\e572"; }
+
+.fa-bolt::before {
+  content: "\f0e7"; }
+
+.fa-zap::before {
+  content: "\f0e7"; }
+
+.fa-glass-water::before {
+  content: "\e4f4"; }
+
+.fa-oil-well::before {
+  content: "\e532"; }
+
+.fa-vault::before {
+  content: "\e2c5"; }
+
+.fa-mars::before {
+  content: "\f222"; }
+
+.fa-toilet::before {
+  content: "\f7d8"; }
+
+.fa-plane-circle-xmark::before {
+  content: "\e557"; }
+
+.fa-yen-sign::before {
+  content: "\f157"; }
+
+.fa-cny::before {
+  content: "\f157"; }
+
+.fa-jpy::before {
+  content: "\f157"; }
+
+.fa-rmb::before {
+  content: "\f157"; }
+
+.fa-yen::before {
+  content: "\f157"; }
+
+.fa-ruble-sign::before {
+  content: "\f158"; }
+
+.fa-rouble::before {
+  content: "\f158"; }
+
+.fa-rub::before {
+  content: "\f158"; }
+
+.fa-ruble::before {
+  content: "\f158"; }
+
+.fa-sun::before {
+  content: "\f185"; }
+
+.fa-guitar::before {
+  content: "\f7a6"; }
+
+.fa-face-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-horse-head::before {
+  content: "\f7ab"; }
+
+.fa-bore-hole::before {
+  content: "\e4c3"; }
+
+.fa-industry::before {
+  content: "\f275"; }
+
+.fa-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrow-alt-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrows-turn-to-dots::before {
+  content: "\e4c1"; }
+
+.fa-florin-sign::before {
+  content: "\e184"; }
+
+.fa-arrow-down-short-wide::before {
+  content: "\f884"; }
+
+.fa-sort-amount-desc::before {
+  content: "\f884"; }
+
+.fa-sort-amount-down-alt::before {
+  content: "\f884"; }
+
+.fa-less-than::before {
+  content: "\3c"; }
+
+.fa-angle-down::before {
+  content: "\f107"; }
+
+.fa-car-tunnel::before {
+  content: "\e4de"; }
+
+.fa-head-side-cough::before {
+  content: "\e061"; }
+
+.fa-grip-lines::before {
+  content: "\f7a4"; }
+
+.fa-thumbs-down::before {
+  content: "\f165"; }
+
+.fa-user-lock::before {
+  content: "\f502"; }
+
+.fa-arrow-right-long::before {
+  content: "\f178"; }
+
+.fa-long-arrow-right::before {
+  content: "\f178"; }
+
+.fa-anchor-circle-xmark::before {
+  content: "\e4ac"; }
+
+.fa-ellipsis::before {
+  content: "\f141"; }
+
+.fa-ellipsis-h::before {
+  content: "\f141"; }
+
+.fa-chess-pawn::before {
+  content: "\f443"; }
+
+.fa-kit-medical::before {
+  content: "\f479"; }
+
+.fa-first-aid::before {
+  content: "\f479"; }
+
+.fa-person-through-window::before {
+  content: "\e5a9"; }
+
+.fa-toolbox::before {
+  content: "\f552"; }
+
+.fa-hands-holding-circle::before {
+  content: "\e4fb"; }
+
+.fa-bug::before {
+  content: "\f188"; }
+
+.fa-credit-card::before {
+  content: "\f09d"; }
+
+.fa-credit-card-alt::before {
+  content: "\f09d"; }
+
+.fa-car::before {
+  content: "\f1b9"; }
+
+.fa-automobile::before {
+  content: "\f1b9"; }
+
+.fa-hand-holding-hand::before {
+  content: "\e4f7"; }
+
+.fa-book-open-reader::before {
+  content: "\f5da"; }
+
+.fa-book-reader::before {
+  content: "\f5da"; }
+
+.fa-mountain-sun::before {
+  content: "\e52f"; }
+
+.fa-arrows-left-right-to-line::before {
+  content: "\e4ba"; }
+
+.fa-dice-d20::before {
+  content: "\f6cf"; }
+
+.fa-truck-droplet::before {
+  content: "\e58c"; }
+
+.fa-file-circle-xmark::before {
+  content: "\e5a1"; }
+
+.fa-temperature-arrow-up::before {
+  content: "\e040"; }
+
+.fa-temperature-up::before {
+  content: "\e040"; }
+
+.fa-medal::before {
+  content: "\f5a2"; }
+
+.fa-bed::before {
+  content: "\f236"; }
+
+.fa-square-h::before {
+  content: "\f0fd"; }
+
+.fa-h-square::before {
+  content: "\f0fd"; }
+
+.fa-podcast::before {
+  content: "\f2ce"; }
+
+.fa-temperature-full::before {
+  content: "\f2c7"; }
+
+.fa-temperature-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-full::before {
+  content: "\f2c7"; }
+
+.fa-bell::before {
+  content: "\f0f3"; }
+
+.fa-superscript::before {
+  content: "\f12b"; }
+
+.fa-plug-circle-xmark::before {
+  content: "\e560"; }
+
+.fa-star-of-life::before {
+  content: "\f621"; }
+
+.fa-phone-slash::before {
+  content: "\f3dd"; }
+
+.fa-paint-roller::before {
+  content: "\f5aa"; }
+
+.fa-handshake-angle::before {
+  content: "\f4c4"; }
+
+.fa-hands-helping::before {
+  content: "\f4c4"; }
+
+.fa-location-dot::before {
+  content: "\f3c5"; }
+
+.fa-map-marker-alt::before {
+  content: "\f3c5"; }
+
+.fa-file::before {
+  content: "\f15b"; }
+
+.fa-greater-than::before {
+  content: "\3e"; }
+
+.fa-person-swimming::before {
+  content: "\f5c4"; }
+
+.fa-swimmer::before {
+  content: "\f5c4"; }
+
+.fa-arrow-down::before {
+  content: "\f063"; }
+
+.fa-droplet::before {
+  content: "\f043"; }
+
+.fa-tint::before {
+  content: "\f043"; }
+
+.fa-eraser::before {
+  content: "\f12d"; }
+
+.fa-earth-americas::before {
+  content: "\f57d"; }
+
+.fa-earth::before {
+  content: "\f57d"; }
+
+.fa-earth-america::before {
+  content: "\f57d"; }
+
+.fa-globe-americas::before {
+  content: "\f57d"; }
+
+.fa-person-burst::before {
+  content: "\e53b"; }
+
+.fa-dove::before {
+  content: "\f4ba"; }
+
+.fa-battery-empty::before {
+  content: "\f244"; }
+
+.fa-battery-0::before {
+  content: "\f244"; }
+
+.fa-socks::before {
+  content: "\f696"; }
+
+.fa-inbox::before {
+  content: "\f01c"; }
+
+.fa-section::before {
+  content: "\e447"; }
+
+.fa-gauge-high::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt-fast::before {
+  content: "\f625"; }
+
+.fa-envelope-open-text::before {
+  content: "\f658"; }
+
+.fa-hospital::before {
+  content: "\f0f8"; }
+
+.fa-hospital-alt::before {
+  content: "\f0f8"; }
+
+.fa-hospital-wide::before {
+  content: "\f0f8"; }
+
+.fa-wine-bottle::before {
+  content: "\f72f"; }
+
+.fa-chess-rook::before {
+  content: "\f447"; }
+
+.fa-bars-staggered::before {
+  content: "\f550"; }
+
+.fa-reorder::before {
+  content: "\f550"; }
+
+.fa-stream::before {
+  content: "\f550"; }
+
+.fa-dharmachakra::before {
+  content: "\f655"; }
+
+.fa-hotdog::before {
+  content: "\f80f"; }
+
+.fa-person-walking-with-cane::before {
+  content: "\f29d"; }
+
+.fa-blind::before {
+  content: "\f29d"; }
+
+.fa-drum::before {
+  content: "\f569"; }
+
+.fa-ice-cream::before {
+  content: "\f810"; }
+
+.fa-heart-circle-bolt::before {
+  content: "\e4fc"; }
+
+.fa-fax::before {
+  content: "\f1ac"; }
+
+.fa-paragraph::before {
+  content: "\f1dd"; }
+
+.fa-check-to-slot::before {
+  content: "\f772"; }
+
+.fa-vote-yea::before {
+  content: "\f772"; }
+
+.fa-star-half::before {
+  content: "\f089"; }
+
+.fa-boxes-stacked::before {
+  content: "\f468"; }
+
+.fa-boxes::before {
+  content: "\f468"; }
+
+.fa-boxes-alt::before {
+  content: "\f468"; }
+
+.fa-link::before {
+  content: "\f0c1"; }
+
+.fa-chain::before {
+  content: "\f0c1"; }
+
+.fa-ear-listen::before {
+  content: "\f2a2"; }
+
+.fa-assistive-listening-systems::before {
+  content: "\f2a2"; }
+
+.fa-tree-city::before {
+  content: "\e587"; }
+
+.fa-play::before {
+  content: "\f04b"; }
+
+.fa-font::before {
+  content: "\f031"; }
+
+.fa-table-cells-row-lock::before {
+  content: "\e67a"; }
+
+.fa-rupiah-sign::before {
+  content: "\e23d"; }
+
+.fa-magnifying-glass::before {
+  content: "\f002"; }
+
+.fa-search::before {
+  content: "\f002"; }
+
+.fa-table-tennis-paddle-ball::before {
+  content: "\f45d"; }
+
+.fa-ping-pong-paddle-ball::before {
+  content: "\f45d"; }
+
+.fa-table-tennis::before {
+  content: "\f45d"; }
+
+.fa-person-dots-from-line::before {
+  content: "\f470"; }
+
+.fa-diagnoses::before {
+  content: "\f470"; }
+
+.fa-trash-can-arrow-up::before {
+  content: "\f82a"; }
+
+.fa-trash-restore-alt::before {
+  content: "\f82a"; }
+
+.fa-naira-sign::before {
+  content: "\e1f6"; }
+
+.fa-cart-arrow-down::before {
+  content: "\f218"; }
+
+.fa-walkie-talkie::before {
+  content: "\f8ef"; }
+
+.fa-file-pen::before {
+  content: "\f31c"; }
+
+.fa-file-edit::before {
+  content: "\f31c"; }
+
+.fa-receipt::before {
+  content: "\f543"; }
+
+.fa-square-pen::before {
+  content: "\f14b"; }
+
+.fa-pen-square::before {
+  content: "\f14b"; }
+
+.fa-pencil-square::before {
+  content: "\f14b"; }
+
+.fa-suitcase-rolling::before {
+  content: "\f5c1"; }
+
+.fa-person-circle-exclamation::before {
+  content: "\e53f"; }
+
+.fa-chevron-down::before {
+  content: "\f078"; }
+
+.fa-battery-full::before {
+  content: "\f240"; }
+
+.fa-battery::before {
+  content: "\f240"; }
+
+.fa-battery-5::before {
+  content: "\f240"; }
+
+.fa-skull-crossbones::before {
+  content: "\f714"; }
+
+.fa-code-compare::before {
+  content: "\e13a"; }
+
+.fa-list-ul::before {
+  content: "\f0ca"; }
+
+.fa-list-dots::before {
+  content: "\f0ca"; }
+
+.fa-school-lock::before {
+  content: "\e56f"; }
+
+.fa-tower-cell::before {
+  content: "\e585"; }
+
+.fa-down-long::before {
+  content: "\f309"; }
+
+.fa-long-arrow-alt-down::before {
+  content: "\f309"; }
+
+.fa-ranking-star::before {
+  content: "\e561"; }
+
+.fa-chess-king::before {
+  content: "\f43f"; }
+
+.fa-person-harassing::before {
+  content: "\e549"; }
+
+.fa-brazilian-real-sign::before {
+  content: "\e46c"; }
+
+.fa-landmark-dome::before {
+  content: "\f752"; }
+
+.fa-landmark-alt::before {
+  content: "\f752"; }
+
+.fa-arrow-up::before {
+  content: "\f062"; }
+
+.fa-tv::before {
+  content: "\f26c"; }
+
+.fa-television::before {
+  content: "\f26c"; }
+
+.fa-tv-alt::before {
+  content: "\f26c"; }
+
+.fa-shrimp::before {
+  content: "\e448"; }
+
+.fa-list-check::before {
+  content: "\f0ae"; }
+
+.fa-tasks::before {
+  content: "\f0ae"; }
+
+.fa-jug-detergent::before {
+  content: "\e519"; }
+
+.fa-circle-user::before {
+  content: "\f2bd"; }
+
+.fa-user-circle::before {
+  content: "\f2bd"; }
+
+.fa-user-shield::before {
+  content: "\f505"; }
+
+.fa-wind::before {
+  content: "\f72e"; }
+
+.fa-car-burst::before {
+  content: "\f5e1"; }
+
+.fa-car-crash::before {
+  content: "\f5e1"; }
+
+.fa-y::before {
+  content: "\59"; }
+
+.fa-person-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-truck-fast::before {
+  content: "\f48b"; }
+
+.fa-shipping-fast::before {
+  content: "\f48b"; }
+
+.fa-fish::before {
+  content: "\f578"; }
+
+.fa-user-graduate::before {
+  content: "\f501"; }
+
+.fa-circle-half-stroke::before {
+  content: "\f042"; }
+
+.fa-adjust::before {
+  content: "\f042"; }
+
+.fa-clapperboard::before {
+  content: "\e131"; }
+
+.fa-circle-radiation::before {
+  content: "\f7ba"; }
+
+.fa-radiation-alt::before {
+  content: "\f7ba"; }
+
+.fa-baseball::before {
+  content: "\f433"; }
+
+.fa-baseball-ball::before {
+  content: "\f433"; }
+
+.fa-jet-fighter-up::before {
+  content: "\e518"; }
+
+.fa-diagram-project::before {
+  content: "\f542"; }
+
+.fa-project-diagram::before {
+  content: "\f542"; }
+
+.fa-copy::before {
+  content: "\f0c5"; }
+
+.fa-volume-xmark::before {
+  content: "\f6a9"; }
+
+.fa-volume-mute::before {
+  content: "\f6a9"; }
+
+.fa-volume-times::before {
+  content: "\f6a9"; }
+
+.fa-hand-sparkles::before {
+  content: "\e05d"; }
+
+.fa-grip::before {
+  content: "\f58d"; }
+
+.fa-grip-horizontal::before {
+  content: "\f58d"; }
+
+.fa-share-from-square::before {
+  content: "\f14d"; }
+
+.fa-share-square::before {
+  content: "\f14d"; }
+
+.fa-child-combatant::before {
+  content: "\e4e0"; }
+
+.fa-child-rifle::before {
+  content: "\e4e0"; }
+
+.fa-gun::before {
+  content: "\e19b"; }
+
+.fa-square-phone::before {
+  content: "\f098"; }
+
+.fa-phone-square::before {
+  content: "\f098"; }
+
+.fa-plus::before {
+  content: "\2b"; }
+
+.fa-add::before {
+  content: "\2b"; }
+
+.fa-expand::before {
+  content: "\f065"; }
+
+.fa-computer::before {
+  content: "\e4e5"; }
+
+.fa-xmark::before {
+  content: "\f00d"; }
+
+.fa-close::before {
+  content: "\f00d"; }
+
+.fa-multiply::before {
+  content: "\f00d"; }
+
+.fa-remove::before {
+  content: "\f00d"; }
+
+.fa-times::before {
+  content: "\f00d"; }
+
+.fa-arrows-up-down-left-right::before {
+  content: "\f047"; }
+
+.fa-arrows::before {
+  content: "\f047"; }
+
+.fa-chalkboard-user::before {
+  content: "\f51c"; }
+
+.fa-chalkboard-teacher::before {
+  content: "\f51c"; }
+
+.fa-peso-sign::before {
+  content: "\e222"; }
+
+.fa-building-shield::before {
+  content: "\e4d8"; }
+
+.fa-baby::before {
+  content: "\f77c"; }
+
+.fa-users-line::before {
+  content: "\e592"; }
+
+.fa-quote-left::before {
+  content: "\f10d"; }
+
+.fa-quote-left-alt::before {
+  content: "\f10d"; }
+
+.fa-tractor::before {
+  content: "\f722"; }
+
+.fa-trash-arrow-up::before {
+  content: "\f829"; }
+
+.fa-trash-restore::before {
+  content: "\f829"; }
+
+.fa-arrow-down-up-lock::before {
+  content: "\e4b0"; }
+
+.fa-lines-leaning::before {
+  content: "\e51e"; }
+
+.fa-ruler-combined::before {
+  content: "\f546"; }
+
+.fa-copyright::before {
+  content: "\f1f9"; }
+
+.fa-equals::before {
+  content: "\3d"; }
+
+.fa-blender::before {
+  content: "\f517"; }
+
+.fa-teeth::before {
+  content: "\f62e"; }
+
+.fa-shekel-sign::before {
+  content: "\f20b"; }
+
+.fa-ils::before {
+  content: "\f20b"; }
+
+.fa-shekel::before {
+  content: "\f20b"; }
+
+.fa-sheqel::before {
+  content: "\f20b"; }
+
+.fa-sheqel-sign::before {
+  content: "\f20b"; }
+
+.fa-map::before {
+  content: "\f279"; }
+
+.fa-rocket::before {
+  content: "\f135"; }
+
+.fa-photo-film::before {
+  content: "\f87c"; }
+
+.fa-photo-video::before {
+  content: "\f87c"; }
+
+.fa-folder-minus::before {
+  content: "\f65d"; }
+
+.fa-store::before {
+  content: "\f54e"; }
+
+.fa-arrow-trend-up::before {
+  content: "\e098"; }
+
+.fa-plug-circle-minus::before {
+  content: "\e55e"; }
+
+.fa-sign-hanging::before {
+  content: "\f4d9"; }
+
+.fa-sign::before {
+  content: "\f4d9"; }
+
+.fa-bezier-curve::before {
+  content: "\f55b"; }
+
+.fa-bell-slash::before {
+  content: "\f1f6"; }
+
+.fa-tablet::before {
+  content: "\f3fb"; }
+
+.fa-tablet-android::before {
+  content: "\f3fb"; }
+
+.fa-school-flag::before {
+  content: "\e56e"; }
+
+.fa-fill::before {
+  content: "\f575"; }
+
+.fa-angle-up::before {
+  content: "\f106"; }
+
+.fa-drumstick-bite::before {
+  content: "\f6d7"; }
+
+.fa-holly-berry::before {
+  content: "\f7aa"; }
+
+.fa-chevron-left::before {
+  content: "\f053"; }
+
+.fa-bacteria::before {
+  content: "\e059"; }
+
+.fa-hand-lizard::before {
+  content: "\f258"; }
+
+.fa-notdef::before {
+  content: "\e1fe"; }
+
+.fa-disease::before {
+  content: "\f7fa"; }
+
+.fa-briefcase-medical::before {
+  content: "\f469"; }
+
+.fa-genderless::before {
+  content: "\f22d"; }
+
+.fa-chevron-right::before {
+  content: "\f054"; }
+
+.fa-retweet::before {
+  content: "\f079"; }
+
+.fa-car-rear::before {
+  content: "\f5de"; }
+
+.fa-car-alt::before {
+  content: "\f5de"; }
+
+.fa-pump-soap::before {
+  content: "\e06b"; }
+
+.fa-video-slash::before {
+  content: "\f4e2"; }
+
+.fa-battery-quarter::before {
+  content: "\f243"; }
+
+.fa-battery-2::before {
+  content: "\f243"; }
+
+.fa-radio::before {
+  content: "\f8d7"; }
+
+.fa-baby-carriage::before {
+  content: "\f77d"; }
+
+.fa-carriage-baby::before {
+  content: "\f77d"; }
+
+.fa-traffic-light::before {
+  content: "\f637"; }
+
+.fa-thermometer::before {
+  content: "\f491"; }
+
+.fa-vr-cardboard::before {
+  content: "\f729"; }
+
+.fa-hand-middle-finger::before {
+  content: "\f806"; }
+
+.fa-percent::before {
+  content: "\25"; }
+
+.fa-percentage::before {
+  content: "\25"; }
+
+.fa-truck-moving::before {
+  content: "\f4df"; }
+
+.fa-glass-water-droplet::before {
+  content: "\e4f5"; }
+
+.fa-display::before {
+  content: "\e163"; }
+
+.fa-face-smile::before {
+  content: "\f118"; }
+
+.fa-smile::before {
+  content: "\f118"; }
+
+.fa-thumbtack::before {
+  content: "\f08d"; }
+
+.fa-thumb-tack::before {
+  content: "\f08d"; }
+
+.fa-trophy::before {
+  content: "\f091"; }
+
+.fa-person-praying::before {
+  content: "\f683"; }
+
+.fa-pray::before {
+  content: "\f683"; }
+
+.fa-hammer::before {
+  content: "\f6e3"; }
+
+.fa-hand-peace::before {
+  content: "\f25b"; }
+
+.fa-rotate::before {
+  content: "\f2f1"; }
+
+.fa-sync-alt::before {
+  content: "\f2f1"; }
+
+.fa-spinner::before {
+  content: "\f110"; }
+
+.fa-robot::before {
+  content: "\f544"; }
+
+.fa-peace::before {
+  content: "\f67c"; }
+
+.fa-gears::before {
+  content: "\f085"; }
+
+.fa-cogs::before {
+  content: "\f085"; }
+
+.fa-warehouse::before {
+  content: "\f494"; }
+
+.fa-arrow-up-right-dots::before {
+  content: "\e4b7"; }
+
+.fa-splotch::before {
+  content: "\f5bc"; }
+
+.fa-face-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-dice-four::before {
+  content: "\f524"; }
+
+.fa-sim-card::before {
+  content: "\f7c4"; }
+
+.fa-transgender::before {
+  content: "\f225"; }
+
+.fa-transgender-alt::before {
+  content: "\f225"; }
+
+.fa-mercury::before {
+  content: "\f223"; }
+
+.fa-arrow-turn-down::before {
+  content: "\f149"; }
+
+.fa-level-down::before {
+  content: "\f149"; }
+
+.fa-person-falling-burst::before {
+  content: "\e547"; }
+
+.fa-award::before {
+  content: "\f559"; }
+
+.fa-ticket-simple::before {
+  content: "\f3ff"; }
+
+.fa-ticket-alt::before {
+  content: "\f3ff"; }
+
+.fa-building::before {
+  content: "\f1ad"; }
+
+.fa-angles-left::before {
+  content: "\f100"; }
+
+.fa-angle-double-left::before {
+  content: "\f100"; }
+
+.fa-qrcode::before {
+  content: "\f029"; }
+
+.fa-clock-rotate-left::before {
+  content: "\f1da"; }
+
+.fa-history::before {
+  content: "\f1da"; }
+
+.fa-face-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-file-export::before {
+  content: "\f56e"; }
+
+.fa-arrow-right-from-file::before {
+  content: "\f56e"; }
+
+.fa-shield::before {
+  content: "\f132"; }
+
+.fa-shield-blank::before {
+  content: "\f132"; }
+
+.fa-arrow-up-short-wide::before {
+  content: "\f885"; }
+
+.fa-sort-amount-up-alt::before {
+  content: "\f885"; }
+
+.fa-house-medical::before {
+  content: "\e3b2"; }
+
+.fa-golf-ball-tee::before {
+  content: "\f450"; }
+
+.fa-golf-ball::before {
+  content: "\f450"; }
+
+.fa-circle-chevron-left::before {
+  content: "\f137"; }
+
+.fa-chevron-circle-left::before {
+  content: "\f137"; }
+
+.fa-house-chimney-window::before {
+  content: "\e00d"; }
+
+.fa-pen-nib::before {
+  content: "\f5ad"; }
+
+.fa-tent-arrow-turn-left::before {
+  content: "\e580"; }
+
+.fa-tents::before {
+  content: "\e582"; }
+
+.fa-wand-magic::before {
+  content: "\f0d0"; }
+
+.fa-magic::before {
+  content: "\f0d0"; }
+
+.fa-dog::before {
+  content: "\f6d3"; }
+
+.fa-carrot::before {
+  content: "\f787"; }
+
+.fa-moon::before {
+  content: "\f186"; }
+
+.fa-wine-glass-empty::before {
+  content: "\f5ce"; }
+
+.fa-wine-glass-alt::before {
+  content: "\f5ce"; }
+
+.fa-cheese::before {
+  content: "\f7ef"; }
+
+.fa-yin-yang::before {
+  content: "\f6ad"; }
+
+.fa-music::before {
+  content: "\f001"; }
+
+.fa-code-commit::before {
+  content: "\f386"; }
+
+.fa-temperature-low::before {
+  content: "\f76b"; }
+
+.fa-person-biking::before {
+  content: "\f84a"; }
+
+.fa-biking::before {
+  content: "\f84a"; }
+
+.fa-broom::before {
+  content: "\f51a"; }
+
+.fa-shield-heart::before {
+  content: "\e574"; }
+
+.fa-gopuram::before {
+  content: "\f664"; }
+
+.fa-earth-oceania::before {
+  content: "\e47b"; }
+
+.fa-globe-oceania::before {
+  content: "\e47b"; }
+
+.fa-square-xmark::before {
+  content: "\f2d3"; }
+
+.fa-times-square::before {
+  content: "\f2d3"; }
+
+.fa-xmark-square::before {
+  content: "\f2d3"; }
+
+.fa-hashtag::before {
+  content: "\23"; }
+
+.fa-up-right-and-down-left-from-center::before {
+  content: "\f424"; }
+
+.fa-expand-alt::before {
+  content: "\f424"; }
+
+.fa-oil-can::before {
+  content: "\f613"; }
+
+.fa-t::before {
+  content: "\54"; }
+
+.fa-hippo::before {
+  content: "\f6ed"; }
+
+.fa-chart-column::before {
+  content: "\e0e3"; }
+
+.fa-infinity::before {
+  content: "\f534"; }
+
+.fa-vial-circle-check::before {
+  content: "\e596"; }
+
+.fa-person-arrow-down-to-line::before {
+  content: "\e538"; }
+
+.fa-voicemail::before {
+  content: "\f897"; }
+
+.fa-fan::before {
+  content: "\f863"; }
+
+.fa-person-walking-luggage::before {
+  content: "\e554"; }
+
+.fa-up-down::before {
+  content: "\f338"; }
+
+.fa-arrows-alt-v::before {
+  content: "\f338"; }
+
+.fa-cloud-moon-rain::before {
+  content: "\f73c"; }
+
+.fa-calendar::before {
+  content: "\f133"; }
+
+.fa-trailer::before {
+  content: "\e041"; }
+
+.fa-bahai::before {
+  content: "\f666"; }
+
+.fa-haykal::before {
+  content: "\f666"; }
+
+.fa-sd-card::before {
+  content: "\f7c2"; }
+
+.fa-dragon::before {
+  content: "\f6d5"; }
+
+.fa-shoe-prints::before {
+  content: "\f54b"; }
+
+.fa-circle-plus::before {
+  content: "\f055"; }
+
+.fa-plus-circle::before {
+  content: "\f055"; }
+
+.fa-face-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-hand-holding::before {
+  content: "\f4bd"; }
+
+.fa-plug-circle-exclamation::before {
+  content: "\e55d"; }
+
+.fa-link-slash::before {
+  content: "\f127"; }
+
+.fa-chain-broken::before {
+  content: "\f127"; }
+
+.fa-chain-slash::before {
+  content: "\f127"; }
+
+.fa-unlink::before {
+  content: "\f127"; }
+
+.fa-clone::before {
+  content: "\f24d"; }
+
+.fa-person-walking-arrow-loop-left::before {
+  content: "\e551"; }
+
+.fa-arrow-up-z-a::before {
+  content: "\f882"; }
+
+.fa-sort-alpha-up-alt::before {
+  content: "\f882"; }
+
+.fa-fire-flame-curved::before {
+  content: "\f7e4"; }
+
+.fa-fire-alt::before {
+  content: "\f7e4"; }
+
+.fa-tornado::before {
+  content: "\f76f"; }
+
+.fa-file-circle-plus::before {
+  content: "\e494"; }
+
+.fa-book-quran::before {
+  content: "\f687"; }
+
+.fa-quran::before {
+  content: "\f687"; }
+
+.fa-anchor::before {
+  content: "\f13d"; }
+
+.fa-border-all::before {
+  content: "\f84c"; }
+
+.fa-face-angry::before {
+  content: "\f556"; }
+
+.fa-angry::before {
+  content: "\f556"; }
+
+.fa-cookie-bite::before {
+  content: "\f564"; }
+
+.fa-arrow-trend-down::before {
+  content: "\e097"; }
+
+.fa-rss::before {
+  content: "\f09e"; }
+
+.fa-feed::before {
+  content: "\f09e"; }
+
+.fa-draw-polygon::before {
+  content: "\f5ee"; }
+
+.fa-scale-balanced::before {
+  content: "\f24e"; }
+
+.fa-balance-scale::before {
+  content: "\f24e"; }
+
+.fa-gauge-simple-high::before {
+  content: "\f62a"; }
+
+.fa-tachometer::before {
+  content: "\f62a"; }
+
+.fa-tachometer-fast::before {
+  content: "\f62a"; }
+
+.fa-shower::before {
+  content: "\f2cc"; }
+
+.fa-desktop::before {
+  content: "\f390"; }
+
+.fa-desktop-alt::before {
+  content: "\f390"; }
+
+.fa-m::before {
+  content: "\4d"; }
+
+.fa-table-list::before {
+  content: "\f00b"; }
+
+.fa-th-list::before {
+  content: "\f00b"; }
+
+.fa-comment-sms::before {
+  content: "\f7cd"; }
+
+.fa-sms::before {
+  content: "\f7cd"; }
+
+.fa-book::before {
+  content: "\f02d"; }
+
+.fa-user-plus::before {
+  content: "\f234"; }
+
+.fa-check::before {
+  content: "\f00c"; }
+
+.fa-battery-three-quarters::before {
+  content: "\f241"; }
+
+.fa-battery-4::before {
+  content: "\f241"; }
+
+.fa-house-circle-check::before {
+  content: "\e509"; }
+
+.fa-angle-left::before {
+  content: "\f104"; }
+
+.fa-diagram-successor::before {
+  content: "\e47a"; }
+
+.fa-truck-arrow-right::before {
+  content: "\e58b"; }
+
+.fa-arrows-split-up-and-left::before {
+  content: "\e4bc"; }
+
+.fa-hand-fist::before {
+  content: "\f6de"; }
+
+.fa-fist-raised::before {
+  content: "\f6de"; }
+
+.fa-cloud-moon::before {
+  content: "\f6c3"; }
+
+.fa-briefcase::before {
+  content: "\f0b1"; }
+
+.fa-person-falling::before {
+  content: "\e546"; }
+
+.fa-image-portrait::before {
+  content: "\f3e0"; }
+
+.fa-portrait::before {
+  content: "\f3e0"; }
+
+.fa-user-tag::before {
+  content: "\f507"; }
+
+.fa-rug::before {
+  content: "\e569"; }
+
+.fa-earth-europe::before {
+  content: "\f7a2"; }
+
+.fa-globe-europe::before {
+  content: "\f7a2"; }
+
+.fa-cart-flatbed-suitcase::before {
+  content: "\f59d"; }
+
+.fa-luggage-cart::before {
+  content: "\f59d"; }
+
+.fa-rectangle-xmark::before {
+  content: "\f410"; }
+
+.fa-rectangle-times::before {
+  content: "\f410"; }
+
+.fa-times-rectangle::before {
+  content: "\f410"; }
+
+.fa-window-close::before {
+  content: "\f410"; }
+
+.fa-baht-sign::before {
+  content: "\e0ac"; }
+
+.fa-book-open::before {
+  content: "\f518"; }
+
+.fa-book-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-handcuffs::before {
+  content: "\e4f8"; }
+
+.fa-triangle-exclamation::before {
+  content: "\f071"; }
+
+.fa-exclamation-triangle::before {
+  content: "\f071"; }
+
+.fa-warning::before {
+  content: "\f071"; }
+
+.fa-database::before {
+  content: "\f1c0"; }
+
+.fa-share::before {
+  content: "\f064"; }
+
+.fa-mail-forward::before {
+  content: "\f064"; }
+
+.fa-bottle-droplet::before {
+  content: "\e4c4"; }
+
+.fa-mask-face::before {
+  content: "\e1d7"; }
+
+.fa-hill-rockslide::before {
+  content: "\e508"; }
+
+.fa-right-left::before {
+  content: "\f362"; }
+
+.fa-exchange-alt::before {
+  content: "\f362"; }
+
+.fa-paper-plane::before {
+  content: "\f1d8"; }
+
+.fa-road-circle-exclamation::before {
+  content: "\e565"; }
+
+.fa-dungeon::before {
+  content: "\f6d9"; }
+
+.fa-align-right::before {
+  content: "\f038"; }
+
+.fa-money-bill-1-wave::before {
+  content: "\f53b"; }
+
+.fa-money-bill-wave-alt::before {
+  content: "\f53b"; }
+
+.fa-life-ring::before {
+  content: "\f1cd"; }
+
+.fa-hands::before {
+  content: "\f2a7"; }
+
+.fa-sign-language::before {
+  content: "\f2a7"; }
+
+.fa-signing::before {
+  content: "\f2a7"; }
+
+.fa-calendar-day::before {
+  content: "\f783"; }
+
+.fa-water-ladder::before {
+  content: "\f5c5"; }
+
+.fa-ladder-water::before {
+  content: "\f5c5"; }
+
+.fa-swimming-pool::before {
+  content: "\f5c5"; }
+
+.fa-arrows-up-down::before {
+  content: "\f07d"; }
+
+.fa-arrows-v::before {
+  content: "\f07d"; }
+
+.fa-face-grimace::before {
+  content: "\f57f"; }
+
+.fa-grimace::before {
+  content: "\f57f"; }
+
+.fa-wheelchair-move::before {
+  content: "\e2ce"; }
+
+.fa-wheelchair-alt::before {
+  content: "\e2ce"; }
+
+.fa-turn-down::before {
+  content: "\f3be"; }
+
+.fa-level-down-alt::before {
+  content: "\f3be"; }
+
+.fa-person-walking-arrow-right::before {
+  content: "\e552"; }
+
+.fa-square-envelope::before {
+  content: "\f199"; }
+
+.fa-envelope-square::before {
+  content: "\f199"; }
+
+.fa-dice::before {
+  content: "\f522"; }
+
+.fa-bowling-ball::before {
+  content: "\f436"; }
+
+.fa-brain::before {
+  content: "\f5dc"; }
+
+.fa-bandage::before {
+  content: "\f462"; }
+
+.fa-band-aid::before {
+  content: "\f462"; }
+
+.fa-calendar-minus::before {
+  content: "\f272"; }
+
+.fa-circle-xmark::before {
+  content: "\f057"; }
+
+.fa-times-circle::before {
+  content: "\f057"; }
+
+.fa-xmark-circle::before {
+  content: "\f057"; }
+
+.fa-gifts::before {
+  content: "\f79c"; }
+
+.fa-hotel::before {
+  content: "\f594"; }
+
+.fa-earth-asia::before {
+  content: "\f57e"; }
+
+.fa-globe-asia::before {
+  content: "\f57e"; }
+
+.fa-id-card-clip::before {
+  content: "\f47f"; }
+
+.fa-id-card-alt::before {
+  content: "\f47f"; }
+
+.fa-magnifying-glass-plus::before {
+  content: "\f00e"; }
+
+.fa-search-plus::before {
+  content: "\f00e"; }
+
+.fa-thumbs-up::before {
+  content: "\f164"; }
+
+.fa-user-clock::before {
+  content: "\f4fd"; }
+
+.fa-hand-dots::before {
+  content: "\f461"; }
+
+.fa-allergies::before {
+  content: "\f461"; }
+
+.fa-file-invoice::before {
+  content: "\f570"; }
+
+.fa-window-minimize::before {
+  content: "\f2d1"; }
+
+.fa-mug-saucer::before {
+  content: "\f0f4"; }
+
+.fa-coffee::before {
+  content: "\f0f4"; }
+
+.fa-brush::before {
+  content: "\f55d"; }
+
+.fa-mask::before {
+  content: "\f6fa"; }
+
+.fa-magnifying-glass-minus::before {
+  content: "\f010"; }
+
+.fa-search-minus::before {
+  content: "\f010"; }
+
+.fa-ruler-vertical::before {
+  content: "\f548"; }
+
+.fa-user-large::before {
+  content: "\f406"; }
+
+.fa-user-alt::before {
+  content: "\f406"; }
+
+.fa-train-tram::before {
+  content: "\e5b4"; }
+
+.fa-user-nurse::before {
+  content: "\f82f"; }
+
+.fa-syringe::before {
+  content: "\f48e"; }
+
+.fa-cloud-sun::before {
+  content: "\f6c4"; }
+
+.fa-stopwatch-20::before {
+  content: "\e06f"; }
+
+.fa-square-full::before {
+  content: "\f45c"; }
+
+.fa-magnet::before {
+  content: "\f076"; }
+
+.fa-jar::before {
+  content: "\e516"; }
+
+.fa-note-sticky::before {
+  content: "\f249"; }
+
+.fa-sticky-note::before {
+  content: "\f249"; }
+
+.fa-bug-slash::before {
+  content: "\e490"; }
+
+.fa-arrow-up-from-water-pump::before {
+  content: "\e4b6"; }
+
+.fa-bone::before {
+  content: "\f5d7"; }
+
+.fa-user-injured::before {
+  content: "\f728"; }
+
+.fa-face-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-plane::before {
+  content: "\f072"; }
+
+.fa-tent-arrows-down::before {
+  content: "\e581"; }
+
+.fa-exclamation::before {
+  content: "\21"; }
+
+.fa-arrows-spin::before {
+  content: "\e4bb"; }
+
+.fa-print::before {
+  content: "\f02f"; }
+
+.fa-turkish-lira-sign::before {
+  content: "\e2bb"; }
+
+.fa-try::before {
+  content: "\e2bb"; }
+
+.fa-turkish-lira::before {
+  content: "\e2bb"; }
+
+.fa-dollar-sign::before {
+  content: "\24"; }
+
+.fa-dollar::before {
+  content: "\24"; }
+
+.fa-usd::before {
+  content: "\24"; }
+
+.fa-x::before {
+  content: "\58"; }
+
+.fa-magnifying-glass-dollar::before {
+  content: "\f688"; }
+
+.fa-search-dollar::before {
+  content: "\f688"; }
+
+.fa-users-gear::before {
+  content: "\f509"; }
+
+.fa-users-cog::before {
+  content: "\f509"; }
+
+.fa-person-military-pointing::before {
+  content: "\e54a"; }
+
+.fa-building-columns::before {
+  content: "\f19c"; }
+
+.fa-bank::before {
+  content: "\f19c"; }
+
+.fa-institution::before {
+  content: "\f19c"; }
+
+.fa-museum::before {
+  content: "\f19c"; }
+
+.fa-university::before {
+  content: "\f19c"; }
+
+.fa-umbrella::before {
+  content: "\f0e9"; }
+
+.fa-trowel::before {
+  content: "\e589"; }
+
+.fa-d::before {
+  content: "\44"; }
+
+.fa-stapler::before {
+  content: "\e5af"; }
+
+.fa-masks-theater::before {
+  content: "\f630"; }
+
+.fa-theater-masks::before {
+  content: "\f630"; }
+
+.fa-kip-sign::before {
+  content: "\e1c4"; }
+
+.fa-hand-point-left::before {
+  content: "\f0a5"; }
+
+.fa-handshake-simple::before {
+  content: "\f4c6"; }
+
+.fa-handshake-alt::before {
+  content: "\f4c6"; }
+
+.fa-jet-fighter::before {
+  content: "\f0fb"; }
+
+.fa-fighter-jet::before {
+  content: "\f0fb"; }
+
+.fa-square-share-nodes::before {
+  content: "\f1e1"; }
+
+.fa-share-alt-square::before {
+  content: "\f1e1"; }
+
+.fa-barcode::before {
+  content: "\f02a"; }
+
+.fa-plus-minus::before {
+  content: "\e43c"; }
+
+.fa-video::before {
+  content: "\f03d"; }
+
+.fa-video-camera::before {
+  content: "\f03d"; }
+
+.fa-graduation-cap::before {
+  content: "\f19d"; }
+
+.fa-mortar-board::before {
+  content: "\f19d"; }
+
+.fa-hand-holding-medical::before {
+  content: "\e05c"; }
+
+.fa-person-circle-check::before {
+  content: "\e53e"; }
+
+.fa-turn-up::before {
+  content: "\f3bf"; }
+
+.fa-level-up-alt::before {
+  content: "\f3bf"; }
+
+.sr-only,
+.fa-sr-only {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+
+.sr-only-focusable:not(:focus),
+.fa-sr-only-focusable:not(:focus) {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+:root, :host {
+  --fa-style-family-brands: 'Font Awesome 6 Brands';
+  --fa-font-brands: normal 400 1em/1 'Font Awesome 6 Brands'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Brands';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+.fab,
+.fa-brands {
+  font-weight: 400; }
+
+.fa-monero:before {
+  content: "\f3d0"; }
+
+.fa-hooli:before {
+  content: "\f427"; }
+
+.fa-yelp:before {
+  content: "\f1e9"; }
+
+.fa-cc-visa:before {
+  content: "\f1f0"; }
+
+.fa-lastfm:before {
+  content: "\f202"; }
+
+.fa-shopware:before {
+  content: "\f5b5"; }
+
+.fa-creative-commons-nc:before {
+  content: "\f4e8"; }
+
+.fa-aws:before {
+  content: "\f375"; }
+
+.fa-redhat:before {
+  content: "\f7bc"; }
+
+.fa-yoast:before {
+  content: "\f2b1"; }
+
+.fa-cloudflare:before {
+  content: "\e07d"; }
+
+.fa-ups:before {
+  content: "\f7e0"; }
+
+.fa-pixiv:before {
+  content: "\e640"; }
+
+.fa-wpexplorer:before {
+  content: "\f2de"; }
+
+.fa-dyalog:before {
+  content: "\f399"; }
+
+.fa-bity:before {
+  content: "\f37a"; }
+
+.fa-stackpath:before {
+  content: "\f842"; }
+
+.fa-buysellads:before {
+  content: "\f20d"; }
+
+.fa-first-order:before {
+  content: "\f2b0"; }
+
+.fa-modx:before {
+  content: "\f285"; }
+
+.fa-guilded:before {
+  content: "\e07e"; }
+
+.fa-vnv:before {
+  content: "\f40b"; }
+
+.fa-square-js:before {
+  content: "\f3b9"; }
+
+.fa-js-square:before {
+  content: "\f3b9"; }
+
+.fa-microsoft:before {
+  content: "\f3ca"; }
+
+.fa-qq:before {
+  content: "\f1d6"; }
+
+.fa-orcid:before {
+  content: "\f8d2"; }
+
+.fa-java:before {
+  content: "\f4e4"; }
+
+.fa-invision:before {
+  content: "\f7b0"; }
+
+.fa-creative-commons-pd-alt:before {
+  content: "\f4ed"; }
+
+.fa-centercode:before {
+  content: "\f380"; }
+
+.fa-glide-g:before {
+  content: "\f2a6"; }
+
+.fa-drupal:before {
+  content: "\f1a9"; }
+
+.fa-jxl:before {
+  content: "\e67b"; }
+
+.fa-hire-a-helper:before {
+  content: "\f3b0"; }
+
+.fa-creative-commons-by:before {
+  content: "\f4e7"; }
+
+.fa-unity:before {
+  content: "\e049"; }
+
+.fa-whmcs:before {
+  content: "\f40d"; }
+
+.fa-rocketchat:before {
+  content: "\f3e8"; }
+
+.fa-vk:before {
+  content: "\f189"; }
+
+.fa-untappd:before {
+  content: "\f405"; }
+
+.fa-mailchimp:before {
+  content: "\f59e"; }
+
+.fa-css3-alt:before {
+  content: "\f38b"; }
+
+.fa-square-reddit:before {
+  content: "\f1a2"; }
+
+.fa-reddit-square:before {
+  content: "\f1a2"; }
+
+.fa-vimeo-v:before {
+  content: "\f27d"; }
+
+.fa-contao:before {
+  content: "\f26d"; }
+
+.fa-square-font-awesome:before {
+  content: "\e5ad"; }
+
+.fa-deskpro:before {
+  content: "\f38f"; }
+
+.fa-brave:before {
+  content: "\e63c"; }
+
+.fa-sistrix:before {
+  content: "\f3ee"; }
+
+.fa-square-instagram:before {
+  content: "\e055"; }
+
+.fa-instagram-square:before {
+  content: "\e055"; }
+
+.fa-battle-net:before {
+  content: "\f835"; }
+
+.fa-the-red-yeti:before {
+  content: "\f69d"; }
+
+.fa-square-hacker-news:before {
+  content: "\f3af"; }
+
+.fa-hacker-news-square:before {
+  content: "\f3af"; }
+
+.fa-edge:before {
+  content: "\f282"; }
+
+.fa-threads:before {
+  content: "\e618"; }
+
+.fa-napster:before {
+  content: "\f3d2"; }
+
+.fa-square-snapchat:before {
+  content: "\f2ad"; }
+
+.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa-google-plus-g:before {
+  content: "\f0d5"; }
+
+.fa-artstation:before {
+  content: "\f77a"; }
+
+.fa-markdown:before {
+  content: "\f60f"; }
+
+.fa-sourcetree:before {
+  content: "\f7d3"; }
+
+.fa-google-plus:before {
+  content: "\f2b3"; }
+
+.fa-diaspora:before {
+  content: "\f791"; }
+
+.fa-foursquare:before {
+  content: "\f180"; }
+
+.fa-stack-overflow:before {
+  content: "\f16c"; }
+
+.fa-github-alt:before {
+  content: "\f113"; }
+
+.fa-phoenix-squadron:before {
+  content: "\f511"; }
+
+.fa-pagelines:before {
+  content: "\f18c"; }
+
+.fa-algolia:before {
+  content: "\f36c"; }
+
+.fa-red-river:before {
+  content: "\f3e3"; }
+
+.fa-creative-commons-sa:before {
+  content: "\f4ef"; }
+
+.fa-safari:before {
+  content: "\f267"; }
+
+.fa-google:before {
+  content: "\f1a0"; }
+
+.fa-square-font-awesome-stroke:before {
+  content: "\f35c"; }
+
+.fa-font-awesome-alt:before {
+  content: "\f35c"; }
+
+.fa-atlassian:before {
+  content: "\f77b"; }
+
+.fa-linkedin-in:before {
+  content: "\f0e1"; }
+
+.fa-digital-ocean:before {
+  content: "\f391"; }
+
+.fa-nimblr:before {
+  content: "\f5a8"; }
+
+.fa-chromecast:before {
+  content: "\f838"; }
+
+.fa-evernote:before {
+  content: "\f839"; }
+
+.fa-hacker-news:before {
+  content: "\f1d4"; }
+
+.fa-creative-commons-sampling:before {
+  content: "\f4f0"; }
+
+.fa-adversal:before {
+  content: "\f36a"; }
+
+.fa-creative-commons:before {
+  content: "\f25e"; }
+
+.fa-watchman-monitoring:before {
+  content: "\e087"; }
+
+.fa-fonticons:before {
+  content: "\f280"; }
+
+.fa-weixin:before {
+  content: "\f1d7"; }
+
+.fa-shirtsinbulk:before {
+  content: "\f214"; }
+
+.fa-codepen:before {
+  content: "\f1cb"; }
+
+.fa-git-alt:before {
+  content: "\f841"; }
+
+.fa-lyft:before {
+  content: "\f3c3"; }
+
+.fa-rev:before {
+  content: "\f5b2"; }
+
+.fa-windows:before {
+  content: "\f17a"; }
+
+.fa-wizards-of-the-coast:before {
+  content: "\f730"; }
+
+.fa-square-viadeo:before {
+  content: "\f2aa"; }
+
+.fa-viadeo-square:before {
+  content: "\f2aa"; }
+
+.fa-meetup:before {
+  content: "\f2e0"; }
+
+.fa-centos:before {
+  content: "\f789"; }
+
+.fa-adn:before {
+  content: "\f170"; }
+
+.fa-cloudsmith:before {
+  content: "\f384"; }
+
+.fa-opensuse:before {
+  content: "\e62b"; }
+
+.fa-pied-piper-alt:before {
+  content: "\f1a8"; }
+
+.fa-square-dribbble:before {
+  content: "\f397"; }
+
+.fa-dribbble-square:before {
+  content: "\f397"; }
+
+.fa-codiepie:before {
+  content: "\f284"; }
+
+.fa-node:before {
+  content: "\f419"; }
+
+.fa-mix:before {
+  content: "\f3cb"; }
+
+.fa-steam:before {
+  content: "\f1b6"; }
+
+.fa-cc-apple-pay:before {
+  content: "\f416"; }
+
+.fa-scribd:before {
+  content: "\f28a"; }
+
+.fa-debian:before {
+  content: "\e60b"; }
+
+.fa-openid:before {
+  content: "\f19b"; }
+
+.fa-instalod:before {
+  content: "\e081"; }
+
+.fa-expeditedssl:before {
+  content: "\f23e"; }
+
+.fa-sellcast:before {
+  content: "\f2da"; }
+
+.fa-square-twitter:before {
+  content: "\f081"; }
+
+.fa-twitter-square:before {
+  content: "\f081"; }
+
+.fa-r-project:before {
+  content: "\f4f7"; }
+
+.fa-delicious:before {
+  content: "\f1a5"; }
+
+.fa-freebsd:before {
+  content: "\f3a4"; }
+
+.fa-vuejs:before {
+  content: "\f41f"; }
+
+.fa-accusoft:before {
+  content: "\f369"; }
+
+.fa-ioxhost:before {
+  content: "\f208"; }
+
+.fa-fonticons-fi:before {
+  content: "\f3a2"; }
+
+.fa-app-store:before {
+  content: "\f36f"; }
+
+.fa-cc-mastercard:before {
+  content: "\f1f1"; }
+
+.fa-itunes-note:before {
+  content: "\f3b5"; }
+
+.fa-golang:before {
+  content: "\e40f"; }
+
+.fa-kickstarter:before {
+  content: "\f3bb"; }
+
+.fa-square-kickstarter:before {
+  content: "\f3bb"; }
+
+.fa-grav:before {
+  content: "\f2d6"; }
+
+.fa-weibo:before {
+  content: "\f18a"; }
+
+.fa-uncharted:before {
+  content: "\e084"; }
+
+.fa-firstdraft:before {
+  content: "\f3a1"; }
+
+.fa-square-youtube:before {
+  content: "\f431"; }
+
+.fa-youtube-square:before {
+  content: "\f431"; }
+
+.fa-wikipedia-w:before {
+  content: "\f266"; }
+
+.fa-wpressr:before {
+  content: "\f3e4"; }
+
+.fa-rendact:before {
+  content: "\f3e4"; }
+
+.fa-angellist:before {
+  content: "\f209"; }
+
+.fa-galactic-republic:before {
+  content: "\f50c"; }
+
+.fa-nfc-directional:before {
+  content: "\e530"; }
+
+.fa-skype:before {
+  content: "\f17e"; }
+
+.fa-joget:before {
+  content: "\f3b7"; }
+
+.fa-fedora:before {
+  content: "\f798"; }
+
+.fa-stripe-s:before {
+  content: "\f42a"; }
+
+.fa-meta:before {
+  content: "\e49b"; }
+
+.fa-laravel:before {
+  content: "\f3bd"; }
+
+.fa-hotjar:before {
+  content: "\f3b1"; }
+
+.fa-bluetooth-b:before {
+  content: "\f294"; }
+
+.fa-square-letterboxd:before {
+  content: "\e62e"; }
+
+.fa-sticker-mule:before {
+  content: "\f3f7"; }
+
+.fa-creative-commons-zero:before {
+  content: "\f4f3"; }
+
+.fa-hips:before {
+  content: "\f452"; }
+
+.fa-behance:before {
+  content: "\f1b4"; }
+
+.fa-reddit:before {
+  content: "\f1a1"; }
+
+.fa-discord:before {
+  content: "\f392"; }
+
+.fa-chrome:before {
+  content: "\f268"; }
+
+.fa-app-store-ios:before {
+  content: "\f370"; }
+
+.fa-cc-discover:before {
+  content: "\f1f2"; }
+
+.fa-wpbeginner:before {
+  content: "\f297"; }
+
+.fa-confluence:before {
+  content: "\f78d"; }
+
+.fa-shoelace:before {
+  content: "\e60c"; }
+
+.fa-mdb:before {
+  content: "\f8ca"; }
+
+.fa-dochub:before {
+  content: "\f394"; }
+
+.fa-accessible-icon:before {
+  content: "\f368"; }
+
+.fa-ebay:before {
+  content: "\f4f4"; }
+
+.fa-amazon:before {
+  content: "\f270"; }
+
+.fa-unsplash:before {
+  content: "\e07c"; }
+
+.fa-yarn:before {
+  content: "\f7e3"; }
+
+.fa-square-steam:before {
+  content: "\f1b7"; }
+
+.fa-steam-square:before {
+  content: "\f1b7"; }
+
+.fa-500px:before {
+  content: "\f26e"; }
+
+.fa-square-vimeo:before {
+  content: "\f194"; }
+
+.fa-vimeo-square:before {
+  content: "\f194"; }
+
+.fa-asymmetrik:before {
+  content: "\f372"; }
+
+.fa-font-awesome:before {
+  content: "\f2b4"; }
+
+.fa-font-awesome-flag:before {
+  content: "\f2b4"; }
+
+.fa-font-awesome-logo-full:before {
+  content: "\f2b4"; }
+
+.fa-gratipay:before {
+  content: "\f184"; }
+
+.fa-apple:before {
+  content: "\f179"; }
+
+.fa-hive:before {
+  content: "\e07f"; }
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+.fa-gitkraken:before {
+  content: "\f3a6"; }
+
+.fa-keybase:before {
+  content: "\f4f5"; }
+
+.fa-apple-pay:before {
+  content: "\f415"; }
+
+.fa-padlet:before {
+  content: "\e4a0"; }
+
+.fa-amazon-pay:before {
+  content: "\f42c"; }
+
+.fa-square-github:before {
+  content: "\f092"; }
+
+.fa-github-square:before {
+  content: "\f092"; }
+
+.fa-stumbleupon:before {
+  content: "\f1a4"; }
+
+.fa-fedex:before {
+  content: "\f797"; }
+
+.fa-phoenix-framework:before {
+  content: "\f3dc"; }
+
+.fa-shopify:before {
+  content: "\e057"; }
+
+.fa-neos:before {
+  content: "\f612"; }
+
+.fa-square-threads:before {
+  content: "\e619"; }
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+.fa-hackerrank:before {
+  content: "\f5f7"; }
+
+.fa-researchgate:before {
+  content: "\f4f8"; }
+
+.fa-swift:before {
+  content: "\f8e1"; }
+
+.fa-angular:before {
+  content: "\f420"; }
+
+.fa-speakap:before {
+  content: "\f3f3"; }
+
+.fa-angrycreative:before {
+  content: "\f36e"; }
+
+.fa-y-combinator:before {
+  content: "\f23b"; }
+
+.fa-empire:before {
+  content: "\f1d1"; }
+
+.fa-envira:before {
+  content: "\f299"; }
+
+.fa-google-scholar:before {
+  content: "\e63b"; }
+
+.fa-square-gitlab:before {
+  content: "\e5ae"; }
+
+.fa-gitlab-square:before {
+  content: "\e5ae"; }
+
+.fa-studiovinari:before {
+  content: "\f3f8"; }
+
+.fa-pied-piper:before {
+  content: "\f2ae"; }
+
+.fa-wordpress:before {
+  content: "\f19a"; }
+
+.fa-product-hunt:before {
+  content: "\f288"; }
+
+.fa-firefox:before {
+  content: "\f269"; }
+
+.fa-linode:before {
+  content: "\f2b8"; }
+
+.fa-goodreads:before {
+  content: "\f3a8"; }
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+  content: "\f264"; }
+
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+  content: "\f264"; }
+
+.fa-jsfiddle:before {
+  content: "\f1cc"; }
+
+.fa-sith:before {
+  content: "\f512"; }
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+.fa-themeisle:before {
+  content: "\f2b2"; }
+
+.fa-page4:before {
+  content: "\f3d7"; }
+
+.fa-hashnode:before {
+  content: "\e499"; }
+
+.fa-react:before {
+  content: "\f41b"; }
+
+.fa-cc-paypal:before {
+  content: "\f1f4"; }
+
+.fa-squarespace:before {
+  content: "\f5be"; }
+
+.fa-cc-stripe:before {
+  content: "\f1f5"; }
+
+.fa-creative-commons-share:before {
+  content: "\f4f2"; }
+
+.fa-bitcoin:before {
+  content: "\f379"; }
+
+.fa-keycdn:before {
+  content: "\f3ba"; }
+
+.fa-opera:before {
+  content: "\f26a"; }
+
+.fa-itch-io:before {
+  content: "\f83a"; }
+
+.fa-umbraco:before {
+  content: "\f8e8"; }
+
+.fa-galactic-senate:before {
+  content: "\f50d"; }
+
+.fa-ubuntu:before {
+  content: "\f7df"; }
+
+.fa-draft2digital:before {
+  content: "\f396"; }
+
+.fa-stripe:before {
+  content: "\f429"; }
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+  content: "\f27c"; }
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+  content: "\f260"; }
+
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+  content: "\f790"; }
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+  content: "\f0d3"; }
+
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+  content: "\f0d3"; }
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+  content: "\f168"; }
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+.fa-blackberry:before {
+  content: "\f37b"; }
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+  content: "\f4ec"; }
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+.fa-playstation:before {
+  content: "\f3df"; }
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+  content: "\f459"; }
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+  content: "\f41d"; }
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+  content: "\f37d"; }
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+.fa-opencart:before {
+  content: "\f23d"; }
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+.fa-vine:before {
+  content: "\f1ca"; }
+
+.fa-signal-messenger:before {
+  content: "\e663"; }
+
+.fa-paypal:before {
+  content: "\f1ed"; }
+
+.fa-gitlab:before {
+  content: "\f296"; }
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+  content: "\f42b"; }
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+  content: "\f281"; }
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+.fa-yahoo:before {
+  content: "\f19e"; }
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+.fa-dailymotion:before {
+  content: "\e052"; }
+
+.fa-affiliatetheme:before {
+  content: "\f36b"; }
+
+.fa-pied-piper-pp:before {
+  content: "\f1a7"; }
+
+.fa-bootstrap:before {
+  content: "\f836"; }
+
+.fa-odnoklassniki:before {
+  content: "\f263"; }
+
+.fa-nfc-symbol:before {
+  content: "\e531"; }
+
+.fa-mintbit:before {
+  content: "\e62f"; }
+
+.fa-ethereum:before {
+  content: "\f42e"; }
+
+.fa-speaker-deck:before {
+  content: "\f83c"; }
+
+.fa-creative-commons-nc-eu:before {
+  content: "\f4e9"; }
+
+.fa-patreon:before {
+  content: "\f3d9"; }
+
+.fa-avianex:before {
+  content: "\f374"; }
+
+.fa-ello:before {
+  content: "\f5f1"; }
+
+.fa-gofore:before {
+  content: "\f3a7"; }
+
+.fa-bimobject:before {
+  content: "\f378"; }
+
+.fa-brave-reverse:before {
+  content: "\e63d"; }
+
+.fa-facebook-f:before {
+  content: "\f39e"; }
+
+.fa-square-google-plus:before {
+  content: "\f0d4"; }
+
+.fa-google-plus-square:before {
+  content: "\f0d4"; }
+
+.fa-web-awesome:before {
+  content: "\e682"; }
+
+.fa-mandalorian:before {
+  content: "\f50f"; }
+
+.fa-first-order-alt:before {
+  content: "\f50a"; }
+
+.fa-osi:before {
+  content: "\f41a"; }
+
+.fa-google-wallet:before {
+  content: "\f1ee"; }
+
+.fa-d-and-d-beyond:before {
+  content: "\f6ca"; }
+
+.fa-periscope:before {
+  content: "\f3da"; }
+
+.fa-fulcrum:before {
+  content: "\f50b"; }
+
+.fa-cloudscale:before {
+  content: "\f383"; }
+
+.fa-forumbee:before {
+  content: "\f211"; }
+
+.fa-mizuni:before {
+  content: "\f3cc"; }
+
+.fa-schlix:before {
+  content: "\f3ea"; }
+
+.fa-square-xing:before {
+  content: "\f169"; }
+
+.fa-xing-square:before {
+  content: "\f169"; }
+
+.fa-bandcamp:before {
+  content: "\f2d5"; }
+
+.fa-wpforms:before {
+  content: "\f298"; }
+
+.fa-cloudversify:before {
+  content: "\f385"; }
+
+.fa-usps:before {
+  content: "\f7e1"; }
+
+.fa-megaport:before {
+  content: "\f5a3"; }
+
+.fa-magento:before {
+  content: "\f3c4"; }
+
+.fa-spotify:before {
+  content: "\f1bc"; }
+
+.fa-optin-monster:before {
+  content: "\f23c"; }
+
+.fa-fly:before {
+  content: "\f417"; }
+
+.fa-aviato:before {
+  content: "\f421"; }
+
+.fa-itunes:before {
+  content: "\f3b4"; }
+
+.fa-cuttlefish:before {
+  content: "\f38c"; }
+
+.fa-blogger:before {
+  content: "\f37c"; }
+
+.fa-flickr:before {
+  content: "\f16e"; }
+
+.fa-viber:before {
+  content: "\f409"; }
+
+.fa-soundcloud:before {
+  content: "\f1be"; }
+
+.fa-digg:before {
+  content: "\f1a6"; }
+
+.fa-tencent-weibo:before {
+  content: "\f1d5"; }
+
+.fa-letterboxd:before {
+  content: "\e62d"; }
+
+.fa-symfony:before {
+  content: "\f83d"; }
+
+.fa-maxcdn:before {
+  content: "\f136"; }
+
+.fa-etsy:before {
+  content: "\f2d7"; }
+
+.fa-facebook-messenger:before {
+  content: "\f39f"; }
+
+.fa-audible:before {
+  content: "\f373"; }
+
+.fa-think-peaks:before {
+  content: "\f731"; }
+
+.fa-bilibili:before {
+  content: "\e3d9"; }
+
+.fa-erlang:before {
+  content: "\f39d"; }
+
+.fa-x-twitter:before {
+  content: "\e61b"; }
+
+.fa-cotton-bureau:before {
+  content: "\f89e"; }
+
+.fa-dashcube:before {
+  content: "\f210"; }
+
+.fa-42-group:before {
+  content: "\e080"; }
+
+.fa-innosoft:before {
+  content: "\e080"; }
+
+.fa-stack-exchange:before {
+  content: "\f18d"; }
+
+.fa-elementor:before {
+  content: "\f430"; }
+
+.fa-square-pied-piper:before {
+  content: "\e01e"; }
+
+.fa-pied-piper-square:before {
+  content: "\e01e"; }
+
+.fa-creative-commons-nd:before {
+  content: "\f4eb"; }
+
+.fa-palfed:before {
+  content: "\f3d8"; }
+
+.fa-superpowers:before {
+  content: "\f2dd"; }
+
+.fa-resolving:before {
+  content: "\f3e7"; }
+
+.fa-xbox:before {
+  content: "\f412"; }
+
+.fa-square-web-awesome-stroke:before {
+  content: "\e684"; }
+
+.fa-searchengin:before {
+  content: "\f3eb"; }
+
+.fa-tiktok:before {
+  content: "\e07b"; }
+
+.fa-square-facebook:before {
+  content: "\f082"; }
+
+.fa-facebook-square:before {
+  content: "\f082"; }
+
+.fa-renren:before {
+  content: "\f18b"; }
+
+.fa-linux:before {
+  content: "\f17c"; }
+
+.fa-glide:before {
+  content: "\f2a5"; }
+
+.fa-linkedin:before {
+  content: "\f08c"; }
+
+.fa-hubspot:before {
+  content: "\f3b2"; }
+
+.fa-deploydog:before {
+  content: "\f38e"; }
+
+.fa-twitch:before {
+  content: "\f1e8"; }
+
+.fa-ravelry:before {
+  content: "\f2d9"; }
+
+.fa-mixer:before {
+  content: "\e056"; }
+
+.fa-square-lastfm:before {
+  content: "\f203"; }
+
+.fa-lastfm-square:before {
+  content: "\f203"; }
+
+.fa-vimeo:before {
+  content: "\f40a"; }
+
+.fa-mendeley:before {
+  content: "\f7b3"; }
+
+.fa-uniregistry:before {
+  content: "\f404"; }
+
+.fa-figma:before {
+  content: "\f799"; }
+
+.fa-creative-commons-remix:before {
+  content: "\f4ee"; }
+
+.fa-cc-amazon-pay:before {
+  content: "\f42d"; }
+
+.fa-dropbox:before {
+  content: "\f16b"; }
+
+.fa-instagram:before {
+  content: "\f16d"; }
+
+.fa-cmplid:before {
+  content: "\e360"; }
+
+.fa-upwork:before {
+  content: "\e641"; }
+
+.fa-facebook:before {
+  content: "\f09a"; }
+
+.fa-gripfire:before {
+  content: "\f3ac"; }
+
+.fa-jedi-order:before {
+  content: "\f50e"; }
+
+.fa-uikit:before {
+  content: "\f403"; }
+
+.fa-fort-awesome-alt:before {
+  content: "\f3a3"; }
+
+.fa-phabricator:before {
+  content: "\f3db"; }
+
+.fa-ussunnah:before {
+  content: "\f407"; }
+
+.fa-earlybirds:before {
+  content: "\f39a"; }
+
+.fa-trade-federation:before {
+  content: "\f513"; }
+
+.fa-autoprefixer:before {
+  content: "\f41c"; }
+
+.fa-whatsapp:before {
+  content: "\f232"; }
+
+.fa-square-upwork:before {
+  content: "\e67c"; }
+
+.fa-slideshare:before {
+  content: "\f1e7"; }
+
+.fa-google-play:before {
+  content: "\f3ab"; }
+
+.fa-viadeo:before {
+  content: "\f2a9"; }
+
+.fa-line:before {
+  content: "\f3c0"; }
+
+.fa-google-drive:before {
+  content: "\f3aa"; }
+
+.fa-servicestack:before {
+  content: "\f3ec"; }
+
+.fa-simplybuilt:before {
+  content: "\f215"; }
+
+.fa-bitbucket:before {
+  content: "\f171"; }
+
+.fa-imdb:before {
+  content: "\f2d8"; }
+
+.fa-deezer:before {
+  content: "\e077"; }
+
+.fa-raspberry-pi:before {
+  content: "\f7bb"; }
+
+.fa-jira:before {
+  content: "\f7b1"; }
+
+.fa-docker:before {
+  content: "\f395"; }
+
+.fa-screenpal:before {
+  content: "\e570"; }
+
+.fa-bluetooth:before {
+  content: "\f293"; }
+
+.fa-gitter:before {
+  content: "\f426"; }
+
+.fa-d-and-d:before {
+  content: "\f38d"; }
+
+.fa-microblog:before {
+  content: "\e01a"; }
+
+.fa-cc-diners-club:before {
+  content: "\f24c"; }
+
+.fa-gg-circle:before {
+  content: "\f261"; }
+
+.fa-pied-piper-hat:before {
+  content: "\f4e5"; }
+
+.fa-kickstarter-k:before {
+  content: "\f3bc"; }
+
+.fa-yandex:before {
+  content: "\f413"; }
+
+.fa-readme:before {
+  content: "\f4d5"; }
+
+.fa-html5:before {
+  content: "\f13b"; }
+
+.fa-sellsy:before {
+  content: "\f213"; }
+
+.fa-square-web-awesome:before {
+  content: "\e683"; }
+
+.fa-sass:before {
+  content: "\f41e"; }
+
+.fa-wirsindhandwerk:before {
+  content: "\e2d0"; }
+
+.fa-wsh:before {
+  content: "\e2d0"; }
+
+.fa-buromobelexperte:before {
+  content: "\f37f"; }
+
+.fa-salesforce:before {
+  content: "\f83b"; }
+
+.fa-octopus-deploy:before {
+  content: "\e082"; }
+
+.fa-medapps:before {
+  content: "\f3c6"; }
+
+.fa-ns8:before {
+  content: "\f3d5"; }
+
+.fa-pinterest-p:before {
+  content: "\f231"; }
+
+.fa-apper:before {
+  content: "\f371"; }
+
+.fa-fort-awesome:before {
+  content: "\f286"; }
+
+.fa-waze:before {
+  content: "\f83f"; }
+
+.fa-bluesky:before {
+  content: "\e671"; }
+
+.fa-cc-jcb:before {
+  content: "\f24b"; }
+
+.fa-snapchat:before {
+  content: "\f2ab"; }
+
+.fa-snapchat-ghost:before {
+  content: "\f2ab"; }
+
+.fa-fantasy-flight-games:before {
+  content: "\f6dc"; }
+
+.fa-rust:before {
+  content: "\e07a"; }
+
+.fa-wix:before {
+  content: "\f5cf"; }
+
+.fa-square-behance:before {
+  content: "\f1b5"; }
+
+.fa-behance-square:before {
+  content: "\f1b5"; }
+
+.fa-supple:before {
+  content: "\f3f9"; }
+
+.fa-webflow:before {
+  content: "\e65c"; }
+
+.fa-rebel:before {
+  content: "\f1d0"; }
+
+.fa-css3:before {
+  content: "\f13c"; }
+
+.fa-staylinked:before {
+  content: "\f3f5"; }
+
+.fa-kaggle:before {
+  content: "\f5fa"; }
+
+.fa-space-awesome:before {
+  content: "\e5ac"; }
+
+.fa-deviantart:before {
+  content: "\f1bd"; }
+
+.fa-cpanel:before {
+  content: "\f388"; }
+
+.fa-goodreads-g:before {
+  content: "\f3a9"; }
+
+.fa-square-git:before {
+  content: "\f1d2"; }
+
+.fa-git-square:before {
+  content: "\f1d2"; }
+
+.fa-square-tumblr:before {
+  content: "\f174"; }
+
+.fa-tumblr-square:before {
+  content: "\f174"; }
+
+.fa-trello:before {
+  content: "\f181"; }
+
+.fa-creative-commons-nc-jp:before {
+  content: "\f4ea"; }
+
+.fa-get-pocket:before {
+  content: "\f265"; }
+
+.fa-perbyte:before {
+  content: "\e083"; }
+
+.fa-grunt:before {
+  content: "\f3ad"; }
+
+.fa-weebly:before {
+  content: "\f5cc"; }
+
+.fa-connectdevelop:before {
+  content: "\f20e"; }
+
+.fa-leanpub:before {
+  content: "\f212"; }
+
+.fa-black-tie:before {
+  content: "\f27e"; }
+
+.fa-themeco:before {
+  content: "\f5c6"; }
+
+.fa-python:before {
+  content: "\f3e2"; }
+
+.fa-android:before {
+  content: "\f17b"; }
+
+.fa-bots:before {
+  content: "\e340"; }
+
+.fa-free-code-camp:before {
+  content: "\f2c5"; }
+
+.fa-hornbill:before {
+  content: "\f592"; }
+
+.fa-js:before {
+  content: "\f3b8"; }
+
+.fa-ideal:before {
+  content: "\e013"; }
+
+.fa-git:before {
+  content: "\f1d3"; }
+
+.fa-dev:before {
+  content: "\f6cc"; }
+
+.fa-sketch:before {
+  content: "\f7c6"; }
+
+.fa-yandex-international:before {
+  content: "\f414"; }
+
+.fa-cc-amex:before {
+  content: "\f1f3"; }
+
+.fa-uber:before {
+  content: "\f402"; }
+
+.fa-github:before {
+  content: "\f09b"; }
+
+.fa-php:before {
+  content: "\f457"; }
+
+.fa-alipay:before {
+  content: "\f642"; }
+
+.fa-youtube:before {
+  content: "\f167"; }
+
+.fa-skyatlas:before {
+  content: "\f216"; }
+
+.fa-firefox-browser:before {
+  content: "\e007"; }
+
+.fa-replyd:before {
+  content: "\f3e6"; }
+
+.fa-suse:before {
+  content: "\f7d6"; }
+
+.fa-jenkins:before {
+  content: "\f3b6"; }
+
+.fa-twitter:before {
+  content: "\f099"; }
+
+.fa-rockrms:before {
+  content: "\f3e9"; }
+
+.fa-pinterest:before {
+  content: "\f0d2"; }
+
+.fa-buffer:before {
+  content: "\f837"; }
+
+.fa-npm:before {
+  content: "\f3d4"; }
+
+.fa-yammer:before {
+  content: "\f840"; }
+
+.fa-btc:before {
+  content: "\f15a"; }
+
+.fa-dribbble:before {
+  content: "\f17d"; }
+
+.fa-stumbleupon-circle:before {
+  content: "\f1a3"; }
+
+.fa-internet-explorer:before {
+  content: "\f26b"; }
+
+.fa-stubber:before {
+  content: "\e5c7"; }
+
+.fa-telegram:before {
+  content: "\f2c6"; }
+
+.fa-telegram-plane:before {
+  content: "\f2c6"; }
+
+.fa-old-republic:before {
+  content: "\f510"; }
+
+.fa-odysee:before {
+  content: "\e5c6"; }
+
+.fa-square-whatsapp:before {
+  content: "\f40c"; }
+
+.fa-whatsapp-square:before {
+  content: "\f40c"; }
+
+.fa-node-js:before {
+  content: "\f3d3"; }
+
+.fa-edge-legacy:before {
+  content: "\e078"; }
+
+.fa-slack:before {
+  content: "\f198"; }
+
+.fa-slack-hash:before {
+  content: "\f198"; }
+
+.fa-medrt:before {
+  content: "\f3c8"; }
+
+.fa-usb:before {
+  content: "\f287"; }
+
+.fa-tumblr:before {
+  content: "\f173"; }
+
+.fa-vaadin:before {
+  content: "\f408"; }
+
+.fa-quora:before {
+  content: "\f2c4"; }
+
+.fa-square-x-twitter:before {
+  content: "\e61a"; }
+
+.fa-reacteurope:before {
+  content: "\f75d"; }
+
+.fa-medium:before {
+  content: "\f23a"; }
+
+.fa-medium-m:before {
+  content: "\f23a"; }
+
+.fa-amilia:before {
+  content: "\f36d"; }
+
+.fa-mixcloud:before {
+  content: "\f289"; }
+
+.fa-flipboard:before {
+  content: "\f44d"; }
+
+.fa-viacoin:before {
+  content: "\f237"; }
+
+.fa-critical-role:before {
+  content: "\f6c9"; }
+
+.fa-sitrox:before {
+  content: "\e44a"; }
+
+.fa-discourse:before {
+  content: "\f393"; }
+
+.fa-joomla:before {
+  content: "\f1aa"; }
+
+.fa-mastodon:before {
+  content: "\f4f6"; }
+
+.fa-airbnb:before {
+  content: "\f834"; }
+
+.fa-wolf-pack-battalion:before {
+  content: "\f514"; }
+
+.fa-buy-n-large:before {
+  content: "\f8a6"; }
+
+.fa-gulp:before {
+  content: "\f3ae"; }
+
+.fa-creative-commons-sampling-plus:before {
+  content: "\f4f1"; }
+
+.fa-strava:before {
+  content: "\f428"; }
+
+.fa-ember:before {
+  content: "\f423"; }
+
+.fa-canadian-maple-leaf:before {
+  content: "\f785"; }
+
+.fa-teamspeak:before {
+  content: "\f4f9"; }
+
+.fa-pushed:before {
+  content: "\f3e1"; }
+
+.fa-wordpress-simple:before {
+  content: "\f411"; }
+
+.fa-nutritionix:before {
+  content: "\f3d6"; }
+
+.fa-wodu:before {
+  content: "\e088"; }
+
+.fa-google-pay:before {
+  content: "\e079"; }
+
+.fa-intercom:before {
+  content: "\f7af"; }
+
+.fa-zhihu:before {
+  content: "\f63f"; }
+
+.fa-korvue:before {
+  content: "\f42f"; }
+
+.fa-pix:before {
+  content: "\e43a"; }
+
+.fa-steam-symbol:before {
+  content: "\f3f6"; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-regular: normal 400 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+.far,
+.fa-regular {
+  font-weight: 400; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-solid: normal 900 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 900;
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+.fas,
+.fa-solid {
+  font-weight: 900; }
+@font-face {
+  font-family: 'Font Awesome 5 Brands';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 900;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-v4compatibility.woff2") format("woff2"), url("../webfonts/fa-v4compatibility.ttf") format("truetype"); }
diff --git a/main/deps/font-awesome-6.5.2/css/all.min.css b/main/deps/font-awesome-6.5.2/css/all.min.css
new file mode 100644
index 00000000..269bceea
--- /dev/null
+++ b/main/deps/font-awesome-6.5.2/css/all.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
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diff --git a/main/deps/font-awesome-6.5.2/css/v4-shims.css b/main/deps/font-awesome-6.5.2/css/v4-shims.css
new file mode 100644
index 00000000..ea60ea4d
--- /dev/null
+++ b/main/deps/font-awesome-6.5.2/css/v4-shims.css
@@ -0,0 +1,2194 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
+.fa.fa-glass:before {
+  content: "\f000"; }
+
+.fa.fa-envelope-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-o:before {
+  content: "\f0e0"; }
+
+.fa.fa-star-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-o:before {
+  content: "\f005"; }
+
+.fa.fa-remove:before {
+  content: "\f00d"; }
+
+.fa.fa-close:before {
+  content: "\f00d"; }
+
+.fa.fa-gear:before {
+  content: "\f013"; }
+
+.fa.fa-trash-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-trash-o:before {
+  content: "\f2ed"; }
+
+.fa.fa-home:before {
+  content: "\f015"; }
+
+.fa.fa-file-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-file-o:before {
+  content: "\f15b"; }
+
+.fa.fa-clock-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-clock-o:before {
+  content: "\f017"; }
+
+.fa.fa-arrow-circle-o-down {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-arrow-circle-o-down:before {
+  content: "\f358"; }
+
+.fa.fa-arrow-circle-o-up {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-arrow-circle-o-up:before {
+  content: "\f35b"; }
+
+.fa.fa-play-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-play-circle-o:before {
+  content: "\f144"; }
+
+.fa.fa-repeat:before {
+  content: "\f01e"; }
+
+.fa.fa-rotate-right:before {
+  content: "\f01e"; }
+
+.fa.fa-refresh:before {
+  content: "\f021"; }
+
+.fa.fa-list-alt {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-list-alt:before {
+  content: "\f022"; }
+
+.fa.fa-dedent:before {
+  content: "\f03b"; }
+
+.fa.fa-video-camera:before {
+  content: "\f03d"; }
+
+.fa.fa-picture-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-picture-o:before {
+  content: "\f03e"; }
+
+.fa.fa-photo {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-photo:before {
+  content: "\f03e"; }
+
+.fa.fa-image {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-image:before {
+  content: "\f03e"; }
+
+.fa.fa-map-marker:before {
+  content: "\f3c5"; }
+
+.fa.fa-pencil-square-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-pencil-square-o:before {
+  content: "\f044"; }
+
+.fa.fa-edit {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-edit:before {
+  content: "\f044"; }
+
+.fa.fa-share-square-o:before {
+  content: "\f14d"; }
+
+.fa.fa-check-square-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-check-square-o:before {
+  content: "\f14a"; }
+
+.fa.fa-arrows:before {
+  content: "\f0b2"; }
+
+.fa.fa-times-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-circle-o:before {
+  content: "\f057"; }
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+.fa.fa-check-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-check-circle-o:before {
+  content: "\f058"; }
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+.fa.fa-mail-forward:before {
+  content: "\f064"; }
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+  font-weight: 400; }
+
+.fa.fa-modx {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fort-awesome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-usb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-product-hunt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-mixcloud {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-scribd {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-pause-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-pause-circle-o:before {
+  content: "\f28b"; }
+
+.fa.fa-stop-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-stop-circle-o:before {
+  content: "\f28d"; }
+
+.fa.fa-bluetooth {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-bluetooth-b {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-gitlab {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpbeginner {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpforms {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-envira {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt:before {
+  content: "\f368"; }
+
+.fa.fa-question-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-question-circle-o:before {
+  content: "\f059"; }
+
+.fa.fa-volume-control-phone:before {
+  content: "\f2a0"; }
+
+.fa.fa-asl-interpreting:before {
+  content: "\f2a3"; }
+
+.fa.fa-deafness:before {
+  content: "\f2a4"; }
+
+.fa.fa-hard-of-hearing:before {
+  content: "\f2a4"; }
+
+.fa.fa-glide {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-glide-g {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-signing:before {
+  content: "\f2a7"; }
+
+.fa.fa-viadeo {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square:before {
+  content: "\f2aa"; }
+
+.fa.fa-snapchat {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost:before {
+  content: "\f2ab"; }
+
+.fa.fa-snapchat-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa.fa-pied-piper {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-first-order {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-yoast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-themeisle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official:before {
+  content: "\f2b3"; }
+
+.fa.fa-google-plus-circle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-circle:before {
+  content: "\f2b3"; }
+
+.fa.fa-font-awesome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa:before {
+  content: "\f2b4"; }
+
+.fa.fa-handshake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-handshake-o:before {
+  content: "\f2b5"; }
+
+.fa.fa-envelope-open-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-open-o:before {
+  content: "\f2b6"; }
+
+.fa.fa-linode {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-address-book-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-book-o:before {
+  content: "\f2b9"; }
+
+.fa.fa-vcard:before {
+  content: "\f2bb"; }
+
+.fa.fa-address-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-card-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-vcard-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-vcard-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-user-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-circle-o:before {
+  content: "\f2bd"; }
+
+.fa.fa-user-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-o:before {
+  content: "\f007"; }
+
+.fa.fa-id-badge {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license:before {
+  content: "\f2c2"; }
+
+.fa.fa-id-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-id-card-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-drivers-license-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-quora {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-free-code-camp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-telegram {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-thermometer-4:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer-3:before {
+  content: "\f2c8"; }
+
+.fa.fa-thermometer-2:before {
+  content: "\f2c9"; }
+
+.fa.fa-thermometer-1:before {
+  content: "\f2ca"; }
+
+.fa.fa-thermometer-0:before {
+  content: "\f2cb"; }
+
+.fa.fa-bathtub:before {
+  content: "\f2cd"; }
+
+.fa.fa-s15:before {
+  content: "\f2cd"; }
+
+.fa.fa-window-maximize {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-restore {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle:before {
+  content: "\f410"; }
+
+.fa.fa-window-close-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-close-o:before {
+  content: "\f410"; }
+
+.fa.fa-times-rectangle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle-o:before {
+  content: "\f410"; }
+
+.fa.fa-bandcamp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-grav {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-etsy {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-imdb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-ravelry {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast:before {
+  content: "\f2da"; }
+
+.fa.fa-snowflake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-snowflake-o:before {
+  content: "\f2dc"; }
+
+.fa.fa-superpowers {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpexplorer {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-meetup {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
diff --git a/main/deps/font-awesome-6.5.2/css/v4-shims.min.css b/main/deps/font-awesome-6.5.2/css/v4-shims.min.css
new file mode 100644
index 00000000..09baf5fc
--- /dev/null
+++ b/main/deps/font-awesome-6.5.2/css/v4-shims.min.css
@@ -0,0 +1,6 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
+.fa.fa-glass:before{content:"\f000"}.fa.fa-envelope-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-envelope-o:before{content:"\f0e0"}.fa.fa-star-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-star-o:before{content:"\f005"}.fa.fa-close:before,.fa.fa-remove:before{content:"\f00d"}.fa.fa-gear:before{content:"\f013"}.fa.fa-trash-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-trash-o:before{content:"\f2ed"}.fa.fa-home:before{content:"\f015"}.fa.fa-file-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-file-o:before{content:"\f15b"}.fa.fa-clock-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-clock-o:before{content:"\f017"}.fa.fa-arrow-circle-o-down{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-arrow-circle-o-down:before{content:"\f358"}.fa.fa-arrow-circle-o-up{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-arrow-circle-o-up:before{content:"\f35b"}.fa.fa-play-circle-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-play-circle-o:before{content:"\f144"}.fa.fa-repeat:before,.fa.fa-rotate-right:before{content:"\f01e"}.fa.fa-refresh:before{content:"\f021"}.fa.fa-list-alt{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-list-alt:before{content:"\f022"}.fa.fa-dedent:before{content:"\f03b"}.fa.fa-video-camera:before{content:"\f03d"}.fa.fa-picture-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-picture-o:before{content:"\f03e"}.fa.fa-photo{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-photo:before{content:"\f03e"}.fa.fa-image{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-image:before{content:"\f03e"}.fa.fa-map-marker:before{content:"\f3c5"}.fa.fa-pencil-square-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-pencil-square-o:before{content:"\f044"}.fa.fa-edit{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-edit:before{content:"\f044"}.fa.fa-share-square-o:before{content:"\f14d"}.fa.fa-check-square-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-check-square-o:before{content:"\f14a"}.fa.fa-arrows:before{content:"\f0b2"}.fa.fa-times-circle-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-times-circle-o:before{content:"\f057"}.fa.fa-check-circle-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-check-circle-o:before{content:"\f058"}.fa.fa-mail-forward:before{content:"\f064"}.fa.fa-expand:before{content:"\f424"}.fa.fa-compress:before{content:"\f422"}.fa.fa-eye,.fa.fa-eye-slash{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-warning:before{content:"\f071"}.fa.fa-calendar:before{content:"\f073"}.fa.fa-arrows-v:before{content:"\f338"}.fa.fa-arrows-h:before{content:"\f337"}.fa.fa-bar-chart-o:before,.fa.fa-bar-chart:before{content:"\e0e3"}.fa.fa-twitter-square{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-twitter-square:before{content:"\f081"}.fa.fa-facebook-square{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-facebook-square:before{content:"\f082"}.fa.fa-gears:before{content:"\f085"}.fa.fa-thumbs-o-up{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-thumbs-o-up:before{content:"\f164"}.fa.fa-thumbs-o-down{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-thumbs-o-down:before{content:"\f165"}.fa.fa-heart-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-heart-o:before{content:"\f004"}.fa.fa-sign-out:before{content:"\f2f5"}.fa.fa-linkedin-square{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-linkedin-square:before{content:"\f08c"}.fa.fa-thumb-tack:before{content:"\f08d"}.fa.fa-external-link:before{content:"\f35d"}.fa.fa-sign-in:before{content:"\f2f6"}.fa.fa-github-square{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-github-square:before{content:"\f092"}.fa.fa-lemon-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-lemon-o:before{content:"\f094"}.fa.fa-square-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-square-o:before{content:"\f0c8"}.fa.fa-bookmark-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-bookmark-o:before{content:"\f02e"}.fa.fa-facebook,.fa.fa-twitter{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-facebook:before{content:"\f39e"}.fa.fa-facebook-f{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-facebook-f:before{content:"\f39e"}.fa.fa-github{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-credit-card{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-feed:before{content:"\f09e"}.fa.fa-hdd-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-hdd-o:before{content:"\f0a0"}.fa.fa-hand-o-right{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-hand-o-right:before{content:"\f0a4"}.fa.fa-hand-o-left{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-hand-o-left:before{content:"\f0a5"}.fa.fa-hand-o-up{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-hand-o-up:before{content:"\f0a6"}.fa.fa-hand-o-down{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-hand-o-down:before{content:"\f0a7"}.fa.fa-globe:before{content:"\f57d"}.fa.fa-tasks:before{content:"\f828"}.fa.fa-arrows-alt:before{content:"\f31e"}.fa.fa-group:before{content:"\f0c0"}.fa.fa-chain:before{content:"\f0c1"}.fa.fa-cut:before{content:"\f0c4"}.fa.fa-files-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-files-o:before{content:"\f0c5"}.fa.fa-floppy-o{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-floppy-o:before{content:"\f0c7"}.fa.fa-save{font-family:"Font Awesome 6 Free";font-weight:400}.fa.fa-save:before{content:"\f0c7"}.fa.fa-navicon:before,.fa.fa-reorder:before{content:"\f0c9"}.fa.fa-magic:before{content:"\e2ca"}.fa.fa-pinterest,.fa.fa-pinterest-square{font-family:"Font Awesome 6 Brands";font-weight:400}.fa.fa-pinterest-square:before{content:"\f0d3"}.fa.fa-google-plus-square{font-family:"Font Awesome 6 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@@ -0,0 +1,7 @@
+/*!
+ * headroom.js v0.11.0 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(n):(t=t||self).Headroom=n()}(this,function(){"use strict";function t(){return"undefined"!=typeof window}function d(t){return function(t){return t&&t.document&&function(t){return 9===t.nodeType}(t.document)}(t)?function(t){var n=t.document,o=n.body,s=n.documentElement;return{scrollHeight:function(){return Math.max(o.scrollHeight,s.scrollHeight,o.offsetHeight,s.offsetHeight,o.clientHeight,s.clientHeight)},height:function(){return t.innerHeight||s.clientHeight||o.clientHeight},scrollY:function(){return void 0!==t.pageYOffset?t.pageYOffset:(s||o.parentNode||o).scrollTop}}}(t):function(t){return{scrollHeight:function(){return Math.max(t.scrollHeight,t.offsetHeight,t.clientHeight)},height:function(){return Math.max(t.offsetHeight,t.clientHeight)},scrollY:function(){return t.scrollTop}}}(t)}function n(t,s,e){var n,o=function(){var n=!1;try{var t={get passive(){n=!0}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){n=!1}return n}(),i=!1,r=d(t),l=r.scrollY(),a={};function c(){var t=Math.round(r.scrollY()),n=r.height(),o=r.scrollHeight();a.scrollY=t,a.lastScrollY=l,a.direction=l<t?"down":"up",a.distance=Math.abs(t-l),a.isOutOfBounds=t<0||o<t+n,a.top=t<=s.offset,a.bottom=o<=t+n,a.toleranceExceeded=a.distance>s.tolerance[a.direction],e(a),l=t,i=!1}function h(){i||(i=!0,n=requestAnimationFrame(c))}var u=!!o&&{passive:!0,capture:!1};return t.addEventListener("scroll",h,u),c(),{destroy:function(){cancelAnimationFrame(n),t.removeEventListener("scroll",h,u)}}}function o(t,n){n=n||{},Object.assign(this,o.options,n),this.classes=Object.assign({},o.options.classes,n.classes),this.elem=t,this.tolerance=function(t){return t===Object(t)?t:{down:t,up:t}}(this.tolerance),this.initialised=!1,this.frozen=!1}return o.prototype={constructor:o,init:function(){return o.cutsTheMustard&&!this.initialised&&(this.addClass("initial"),this.initialised=!0,setTimeout(function(t){t.scrollTracker=n(t.scroller,{offset:t.offset,tolerance:t.tolerance},t.update.bind(t))},100,this)),this},destroy:function(){this.initialised=!1,Object.keys(this.classes).forEach(this.removeClass,this),this.scrollTracker.destroy()},unpin:function(){!this.hasClass("pinned")&&this.hasClass("unpinned")||(this.addClass("unpinned"),this.removeClass("pinned"),this.onUnpin&&this.onUnpin.call(this))},pin:function(){this.hasClass("unpinned")&&(this.addClass("pinned"),this.removeClass("unpinned"),this.onPin&&this.onPin.call(this))},freeze:function(){this.frozen=!0,this.addClass("frozen")},unfreeze:function(){this.frozen=!1,this.removeClass("frozen")},top:function(){this.hasClass("top")||(this.addClass("top"),this.removeClass("notTop"),this.onTop&&this.onTop.call(this))},notTop:function(){this.hasClass("notTop")||(this.addClass("notTop"),this.removeClass("top"),this.onNotTop&&this.onNotTop.call(this))},bottom:function(){this.hasClass("bottom")||(this.addClass("bottom"),this.removeClass("notBottom"),this.onBottom&&this.onBottom.call(this))},notBottom:function(){this.hasClass("notBottom")||(this.addClass("notBottom"),this.removeClass("bottom"),this.onNotBottom&&this.onNotBottom.call(this))},shouldUnpin:function(t){return"down"===t.direction&&!t.top&&t.toleranceExceeded},shouldPin:function(t){return"up"===t.direction&&t.toleranceExceeded||t.top},addClass:function(t){this.elem.classList.add.apply(this.elem.classList,this.classes[t].split(" "))},removeClass:function(t){this.elem.classList.remove.apply(this.elem.classList,this.classes[t].split(" "))},hasClass:function(t){return this.classes[t].split(" ").every(function(t){return this.classList.contains(t)},this.elem)},update:function(t){t.isOutOfBounds||!0!==this.frozen&&(t.top?this.top():this.notTop(),t.bottom?this.bottom():this.notBottom(),this.shouldUnpin(t)?this.unpin():this.shouldPin(t)&&this.pin())}},o.options={tolerance:{up:0,down:0},offset:0,scroller:t()?window:null,classes:{frozen:"headroom--frozen",pinned:"headroom--pinned",unpinned:"headroom--unpinned",top:"headroom--top",notTop:"headroom--not-top",bottom:"headroom--bottom",notBottom:"headroom--not-bottom",initial:"headroom"}},o.cutsTheMustard=!!(t()&&function(){}.bind&&"classList"in document.documentElement&&Object.assign&&Object.keys&&requestAnimationFrame),o});
\ No newline at end of file
diff --git a/main/deps/headroom-0.11.0/jQuery.headroom.min.js b/main/deps/headroom-0.11.0/jQuery.headroom.min.js
new file mode 100644
index 00000000..17f70c9e
--- /dev/null
+++ b/main/deps/headroom-0.11.0/jQuery.headroom.min.js
@@ -0,0 +1,7 @@
+/*!
+ * headroom.js v0.9.4 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery);
\ No newline at end of file
diff --git a/main/deps/search-1.0.0/autocomplete.jquery.min.js b/main/deps/search-1.0.0/autocomplete.jquery.min.js
new file mode 100644
index 00000000..fb63a6a2
--- /dev/null
+++ b/main/deps/search-1.0.0/autocomplete.jquery.min.js
@@ -0,0 +1,7 @@
+/*!
+ * autocomplete.js 0.38.0
+ * https://github.com/algolia/autocomplete.js
+ * Copyright 2020 Algolia, Inc. and other contributors; Licensed MIT
+ */
+!function(a){function b(d){if(c[d])return c[d].exports;var e=c[d]={exports:{},id:d,loaded:!1};return a[d].call(e.exports,e,e.exports,b),e.loaded=!0,e.exports}var c={};b.m=a,b.c=c,b.p="",b(0)}([function(a,b,c){"use strict";a.exports=c(1)},function(a,b,c){"use strict";var d=c(2),e=c(3);d.element=e;var f=c(4);f.isArray=e.isArray,f.isFunction=e.isFunction,f.isObject=e.isPlainObject,f.bind=e.proxy,f.each=function(a,b){function c(a,c){return b(c,a)}e.each(a,c)},f.map=e.map,f.mixin=e.extend,f.Event=e.Event;var g,h,i,j=c(5),k=c(6);g=e.fn.autocomplete,h="aaAutocomplete",i={initialize:function(a,b){function c(){var c,d=e(this),f=new k({el:d});c=new j({input:d,eventBus:f,dropdownMenuContainer:a.dropdownMenuContainer,hint:void 0===a.hint||!!a.hint,minLength:a.minLength,autoselect:a.autoselect,autoselectOnBlur:a.autoselectOnBlur,tabAutocomplete:a.tabAutocomplete,openOnFocus:a.openOnFocus,templates:a.templates,debug:a.debug,clearOnSelected:a.clearOnSelected,cssClasses:a.cssClasses,datasets:b,keyboardShortcuts:a.keyboardShortcuts,appendTo:a.appendTo,autoWidth:a.autoWidth}),d.data(h,c)}return b=f.isArray(b)?b:[].slice.call(arguments,1),a=a||{},this.each(c)},open:function(){function a(){var a,b=e(this);(a=b.data(h))&&a.open()}return this.each(a)},close:function(){function a(){var a,b=e(this);(a=b.data(h))&&a.close()}return this.each(a)},val:function(a){function b(){var b,c=e(this);(b=c.data(h))&&b.setVal(a)}return arguments.length?this.each(b):function(a){var b,c;return(b=a.data(h))&&(c=b.getVal()),c}(this.first())},destroy:function(){function a(){var a,b=e(this);(a=b.data(h))&&(a.destroy(),b.removeData(h))}return this.each(a)}},e.fn.autocomplete=function(a){var b;return i[a]&&"initialize"!==a?(b=this.filter(function(){return!!e(this).data(h)}),i[a].apply(b,[].slice.call(arguments,1))):i.initialize.apply(this,arguments)},e.fn.autocomplete.noConflict=function(){return e.fn.autocomplete=g,this},e.fn.autocomplete.sources=j.sources,e.fn.autocomplete.escapeHighlightedString=f.escapeHighlightedString,a.exports=e.fn.autocomplete},function(a,b){"use strict";a.exports={element:null}},function(a,b){a.exports=jQuery},function(a,b,c){"use strict";function d(a){return a.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g,"\\$&")}var e=c(2);a.exports={isArray:null,isFunction:null,isObject:null,bind:null,each:null,map:null,mixin:null,isMsie:function(a){if(void 0===a&&(a=navigator.userAgent),/(msie|trident)/i.test(a)){var b=a.match(/(msie |rv:)(\d+(.\d+)?)/i);if(b)return b[2]}return!1},escapeRegExChars:function(a){return a.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g,"\\$&")},isNumber:function(a){return"number"==typeof a},toStr:function(a){return void 0===a||null===a?"":a+""},cloneDeep:function(a){var b=this.mixin({},a),c=this;return this.each(b,function(a,d){a&&(c.isArray(a)?b[d]=[].concat(a):c.isObject(a)&&(b[d]=c.cloneDeep(a)))}),b},error:function(a){throw new Error(a)},every:function(a,b){var c=!0;return a?(this.each(a,function(d,e){c&&(c=b.call(null,d,e,a)&&c)}),!!c):c},any:function(a,b){var c=!1;return a?(this.each(a,function(d,e){if(b.call(null,d,e,a))return c=!0,!1}),c):c},getUniqueId:function(){var a=0;return function(){return a++}}(),templatify:function(a){if(this.isFunction(a))return a;var b=e.element(a);return"SCRIPT"===b.prop("tagName")?function(){return b.text()}:function(){return String(a)}},defer:function(a){setTimeout(a,0)},noop:function(){},formatPrefix:function(a,b){return b?"":a+"-"},className:function(a,b,c){return(c?"":".")+a+b},escapeHighlightedString:function(a,b,c){b=b||"<em>";var e=document.createElement("div");e.appendChild(document.createTextNode(b)),c=c||"</em>";var f=document.createElement("div");f.appendChild(document.createTextNode(c));var g=document.createElement("div");return g.appendChild(document.createTextNode(a)),g.innerHTML.replace(RegExp(d(e.innerHTML),"g"),b).replace(RegExp(d(f.innerHTML),"g"),c)}}},function(a,b,c){"use strict";function d(a){var b,c;if(a=a||{},a.input||i.error("missing input"),this.isActivated=!1,this.debug=!!a.debug,this.autoselect=!!a.autoselect,this.autoselectOnBlur=!!a.autoselectOnBlur,this.openOnFocus=!!a.openOnFocus,this.minLength=i.isNumber(a.minLength)?a.minLength:1,this.autoWidth=void 0===a.autoWidth||!!a.autoWidth,this.clearOnSelected=!!a.clearOnSelected,this.tabAutocomplete=void 0===a.tabAutocomplete||!!a.tabAutocomplete,a.hint=!!a.hint,a.hint&&a.appendTo)throw new Error("[autocomplete.js] hint and appendTo options can't be used at the same time");this.css=a.css=i.mixin({},o,a.appendTo?o.appendTo:{}),this.cssClasses=a.cssClasses=i.mixin({},o.defaultClasses,a.cssClasses||{}),this.cssClasses.prefix=a.cssClasses.formattedPrefix=i.formatPrefix(this.cssClasses.prefix,this.cssClasses.noPrefix),this.listboxId=a.listboxId=[this.cssClasses.root,"listbox",i.getUniqueId()].join("-");var f=e(a);this.$node=f.wrapper;var g=this.$input=f.input;b=f.menu,c=f.hint,a.dropdownMenuContainer&&j.element(a.dropdownMenuContainer).css("position","relative").append(b.css("top","0")),g.on("blur.aa",function(a){var c=document.activeElement;i.isMsie()&&(b[0]===c||b[0].contains(c))&&(a.preventDefault(),a.stopImmediatePropagation(),i.defer(function(){g.focus()}))}),b.on("mousedown.aa",function(a){a.preventDefault()}),this.eventBus=a.eventBus||new k({el:g}),this.dropdown=new d.Dropdown({appendTo:a.appendTo,wrapper:this.$node,menu:b,datasets:a.datasets,templates:a.templates,cssClasses:a.cssClasses,minLength:this.minLength}).onSync("suggestionClicked",this._onSuggestionClicked,this).onSync("cursorMoved",this._onCursorMoved,this).onSync("cursorRemoved",this._onCursorRemoved,this).onSync("opened",this._onOpened,this).onSync("closed",this._onClosed,this).onSync("shown",this._onShown,this).onSync("empty",this._onEmpty,this).onSync("redrawn",this._onRedrawn,this).onAsync("datasetRendered",this._onDatasetRendered,this),this.input=new 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g=n.dropdown.replace("%PREFIX%",a.cssClasses.prefix).replace("%DROPDOWN_MENU%",a.cssClasses.dropdownMenu);d=j.element(g).css(a.css.dropdown).attr({role:"listbox",id:a.listboxId}),a.templates&&a.templates.dropdownMenu&&d.html(i.templatify(a.templates.dropdownMenu)()),e=b.clone().css(a.css.hint).css(f(b)),e.val("").addClass(i.className(a.cssClasses.prefix,a.cssClasses.hint,!0)).removeAttr("id name placeholder required").prop("readonly",!0).attr({"aria-hidden":"true",autocomplete:"off",spellcheck:"false",tabindex:-1}),e.removeData&&e.removeData(),b.data(h,{"aria-autocomplete":b.attr("aria-autocomplete"),"aria-expanded":b.attr("aria-expanded"),"aria-owns":b.attr("aria-owns"),autocomplete:b.attr("autocomplete"),dir:b.attr("dir"),role:b.attr("role"),spellcheck:b.attr("spellcheck"),style:b.attr("style"),type:b.attr("type")}),b.addClass(i.className(a.cssClasses.prefix,a.cssClasses.input,!0)).attr({autocomplete:"off",spellcheck:!1,role:"combobox","aria-autocomplete":a.datasets&&a.datasets[0]&&a.datasets[0].displayKey?"both":"list","aria-expanded":"false","aria-label":a.ariaLabel,"aria-owns":a.listboxId}).css(a.hint?a.css.input:a.css.inputWithNoHint);try{b.attr("dir")||b.attr("dir","auto")}catch(a){}return c=a.appendTo?c.appendTo(j.element(a.appendTo).eq(0)).eq(0):b.wrap(c).parent(),c.prepend(a.hint?e:null).append(d),{wrapper:c,input:b,hint:e,menu:d}}function f(a){return{backgroundAttachment:a.css("background-attachment"),backgroundClip:a.css("background-clip"),backgroundColor:a.css("background-color"),backgroundImage:a.css("background-image"),backgroundOrigin:a.css("background-origin"),backgroundPosition:a.css("background-position"),backgroundRepeat:a.css("background-repeat"),backgroundSize:a.css("background-size")}}function g(a,b){var c=a.find(i.className(b.prefix,b.input));i.each(c.data(h),function(a,b){void 0===a?c.removeAttr(b):c.attr(b,a)}),c.detach().removeClass(i.className(b.prefix,b.input,!0)).insertAfter(a),c.removeData&&c.removeData(h),a.remove()}var h="aaAttrs",i=c(4),j=c(2),k=c(6),l=c(7),m=c(16),n=c(18),o=c(19);i.mixin(d.prototype,{_bindKeyboardShortcuts:function(a){if(a.keyboardShortcuts){var b=this.$input,c=[];i.each(a.keyboardShortcuts,function(a){"string"==typeof a&&(a=a.toUpperCase().charCodeAt(0)),c.push(a)}),j.element(document).keydown(function(a){var d=a.target||a.srcElement,e=d.tagName;if(!d.isContentEditable&&"INPUT"!==e&&"SELECT"!==e&&"TEXTAREA"!==e){var f=a.which||a.keyCode;c.indexOf(f)!==-1&&(b.focus(),a.stopPropagation(),a.preventDefault())}})}},_onSuggestionClicked:function(a,b){var c,d={selectionMethod:"click"};(c=this.dropdown.getDatumForSuggestion(b))&&this._select(c,d)},_onCursorMoved:function(a,b){var c=this.dropdown.getDatumForCursor(),d=this.dropdown.getCurrentCursor().attr("id");this.input.setActiveDescendant(d),c&&(b&&this.input.setInputValue(c.value,!0),this.eventBus.trigger("cursorchanged",c.raw,c.datasetName))},_onCursorRemoved:function(){this.input.resetInputValue(),this._updateHint(),this.eventBus.trigger("cursorremoved")},_onDatasetRendered:function(){this._updateHint(),this.eventBus.trigger("updated")},_onOpened:function(){this._updateHint(),this.input.expand(),this.eventBus.trigger("opened")},_onEmpty:function(){this.eventBus.trigger("empty")},_onRedrawn:function(){this.$node.css("top","0px"),this.$node.css("left","0px");var a=this.$input[0].getBoundingClientRect();this.autoWidth&&this.$node.css("width",a.width+"px");var b=this.$node[0].getBoundingClientRect(),c=a.bottom-b.top;this.$node.css("top",c+"px");var d=a.left-b.left;this.$node.css("left",d+"px"),this.eventBus.trigger("redrawn")},_onShown:function(){this.eventBus.trigger("shown"),this.autoselect&&this.dropdown.cursorTopSuggestion()},_onClosed:function(){this.input.clearHint(),this.input.removeActiveDescendant(),this.input.collapse(),this.eventBus.trigger("closed")},_onFocused:function(){if(this.isActivated=!0,this.openOnFocus){var a=this.input.getQuery();a.length>=this.minLength?this.dropdown.update(a):this.dropdown.empty(),this.dropdown.open()}},_onBlurred:function(){var a,b;a=this.dropdown.getDatumForCursor(),b=this.dropdown.getDatumForTopSuggestion();var c={selectionMethod:"blur"};this.debug||(this.autoselectOnBlur&&a?this._select(a,c):this.autoselectOnBlur&&b?this._select(b,c):(this.isActivated=!1,this.dropdown.empty(),this.dropdown.close()))},_onEnterKeyed:function(a,b){var c,d;c=this.dropdown.getDatumForCursor(),d=this.dropdown.getDatumForTopSuggestion();var 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+var c=[].slice.call(arguments,1);this.cacheSuggestions(a,b,c),this._render.apply(this,[a,b].concat(c))}}if(this.query=a,this.canceled=!1,this.shouldFetchFromCache(a))b.apply(this,[this.cachedSuggestions].concat(this.cachedRenderExtraArgs));else{var c=this,d=function(){c.canceled||c.source(a,b.bind(c))};if(this.debounce){var e=function(){c.debounceTimeout=null,d()};clearTimeout(this.debounceTimeout),this.debounceTimeout=setTimeout(e,this.debounce)}else d()}},cacheSuggestions:function(a,b,c){this.cachedQuery=a,this.cachedSuggestions=b,this.cachedRenderExtraArgs=c},shouldFetchFromCache:function(a){return this.cache&&this.cachedQuery===a&&this.cachedSuggestions&&this.cachedSuggestions.length},clearCachedSuggestions:function(){delete this.cachedQuery,delete this.cachedSuggestions,delete this.cachedRenderExtraArgs},cancel:function(){this.canceled=!0},clear:function(){this.$el&&(this.cancel(),this.$el.empty(),this.trigger("rendered",""))},isEmpty:function(){return this._isEmpty},destroy:function(){this.clearCachedSuggestions(),this.$el=null}}),a.exports=d},function(a,b){"use strict";a.exports={wrapper:'<span class="%ROOT%"></span>',dropdown:'<span class="%PREFIX%%DROPDOWN_MENU%"></span>',dataset:'<div class="%PREFIX%%DATASET%-%CLASS%"></div>',suggestions:'<span class="%PREFIX%%SUGGESTIONS%"></span>',suggestion:'<div class="%PREFIX%%SUGGESTION%"></div>'}},function(a,b,c){"use strict";var d=c(4),e={wrapper:{position:"relative",display:"inline-block"},hint:{position:"absolute",top:"0",left:"0",borderColor:"transparent",boxShadow:"none",opacity:"1"},input:{position:"relative",verticalAlign:"top",backgroundColor:"transparent"},inputWithNoHint:{position:"relative",verticalAlign:"top"},dropdown:{position:"absolute",top:"100%",left:"0",zIndex:"100",display:"none"},suggestions:{display:"block"},suggestion:{whiteSpace:"nowrap",cursor:"pointer"},suggestionChild:{whiteSpace:"normal"},ltr:{left:"0",right:"auto"},rtl:{left:"auto",right:"0"},defaultClasses:{root:"algolia-autocomplete",prefix:"aa",noPrefix:!1,dropdownMenu:"dropdown-menu",input:"input",hint:"hint",suggestions:"suggestions",suggestion:"suggestion",cursor:"cursor",dataset:"dataset",empty:"empty"},appendTo:{wrapper:{position:"absolute",zIndex:"100",display:"none"},input:{},inputWithNoHint:{},dropdown:{display:"block"}}};d.isMsie()&&d.mixin(e.input,{backgroundImage:"url(data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)"}),d.isMsie()&&d.isMsie()<=7&&d.mixin(e.input,{marginTop:"-1px"}),a.exports=e},function(a,b,c){"use strict";a.exports={hits:c(21),popularIn:c(24)}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23),g=function(){function a(a,d){return window.Promise.resolve().then(function(){return b.length&&(e=a.search(b),b=[]),e}).then(function(a){if(a)return c=a.results,c[d]})}var b=[],c=[],e=window.Promise.resolve();return function(c,e){return function(f,g){a(c.as,b.push({indexName:c.indexName,query:f,params:e})-1).then(function(a){a&&g(a.hits,a)}).catch(function(a){d.error(a.message)})}}}();a.exports=function(a,b){var c=f(a.as._ua);if(c&&c[0]>=3&&c[1]>20){var d="autocomplete.js "+e;a.as._ua.indexOf(d)===-1&&(a.as._ua+="; "+d)}return g(a,b)}},function(a,b){a.exports="0.38.0"},function(a,b){"use strict";a.exports=function(a){var b=a.match(/Algolia for JavaScript \((\d+\.)(\d+\.)(\d+)\)/)||a.match(/Algolia for vanilla JavaScript (\d+\.)(\d+\.)(\d+)/);if(b)return[b[1],b[2],b[3]]}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23);a.exports=function(a,b,c,g){function h(h,i){a.search(h,b,function(a,h){if(a)return void d.error(a.message);if(h.hits.length>0){var l=h.hits[0],m=d.mixin({hitsPerPage:0},c);delete m.source,delete m.index;var n=f(k.as._ua);return n&&n[0]>=3&&n[1]>20&&(b.additionalUA="autocomplete.js "+e),void k.search(j(l),m,function(a,b){if(a)return void d.error(a.message);var c=[];if(g.includeAll){var e=g.allTitle||"All departments";c.push(d.mixin({facet:{value:e,count:b.nbHits}},d.cloneDeep(l)))}d.each(b.facets,function(a,b){d.each(a,function(a,e){c.push(d.mixin({facet:{facet:b,value:e,count:a}},d.cloneDeep(l)))})});for(var f=1;f<h.hits.length;++f)c.push(h.hits[f]);i(c,h)})}i([])})}var i=f(a.as._ua);if(i&&i[0]>=3&&i[1]>20&&(b=b||{},b.additionalUA="autocomplete.js "+e),!c.source)return d.error("Missing 'source' key");var j=d.isFunction(c.source)?c.source:function(a){return a[c.source]};if(!c.index)return d.error("Missing 'index' key");var k=c.index;return g=g||{},h}}]);
\ No newline at end of file
diff --git a/main/deps/search-1.0.0/fuse.min.js b/main/deps/search-1.0.0/fuse.min.js
new file mode 100644
index 00000000..7def5985
--- /dev/null
+++ b/main/deps/search-1.0.0/fuse.min.js
@@ -0,0 +1,9 @@
+/**
+ * Fuse.js v6.4.6 - Lightweight fuzzy-search (http://fusejs.io)
+ *
+ * Copyright (c) 2021 Kiro Risk (http://kiro.me)
+ * All Rights Reserved. Apache Software License 2.0
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ */
+var e,t;e=this,t=function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(t)}function t(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function n(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}function r(e,t,r){return t&&n(e.prototype,t),r&&n(e,r),e}function i(e,t,n){return t in e?Object.defineProperty(e,t,{value:n,enumerable:!0,configurable:!0,writable:!0}):e[t]=n,e}function o(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),n.push.apply(n,r)}return n}function c(e){for(var t=1;t<arguments.length;t++){var n=null!=arguments[t]?arguments[t]:{};t%2?o(Object(n),!0).forEach((function(t){i(e,t,n[t])})):Object.getOwnPropertyDescriptors?Object.defineProperties(e,Object.getOwnPropertyDescriptors(n)):o(Object(n)).forEach((function(t){Object.defineProperty(e,t,Object.getOwnPropertyDescriptor(n,t))}))}return e}function a(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&u(e,t)}function s(e){return(s=Object.setPrototypeOf?Object.getPrototypeOf:function(e){return e.__proto__||Object.getPrototypeOf(e)})(e)}function u(e,t){return(u=Object.setPrototypeOf||function(e,t){return e.__proto__=t,e})(e,t)}function h(e,t){return!t||"object"!=typeof t&&"function"!=typeof t?function(e){if(void 0===e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return e}(e):t}function f(e){var t=function(){if("undefined"==typeof 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\ No newline at end of file
diff --git a/main/deps/search-1.0.0/mark.min.js b/main/deps/search-1.0.0/mark.min.js
new file mode 100644
index 00000000..1eea0533
--- /dev/null
+++ b/main/deps/search-1.0.0/mark.min.js
@@ -0,0 +1,7 @@
+/*!***************************************************
+* mark.js v8.11.1
+* https://markjs.io/
+* Copyright (c) 2014–2018, Julian Kühnel
+* Released under the MIT license https://git.io/vwTVl
+*****************************************************/
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):e.Mark=t()}(this,function(){"use strict";var e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e},t=function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")},n=function(){function e(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(t,n,r){return n&&e(t.prototype,n),r&&e(t,r),t}}(),r=Object.assign||function(e){for(var t=1;t<arguments.length;t++){var n=arguments[t];for(var r in n)Object.prototype.hasOwnProperty.call(n,r)&&(e[r]=n[r])}return e},i=function(){function e(n){var r=!(arguments.length>1&&void 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 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
+<li class="nav-item"><a class="nav-link" href="articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-home">
 <div class="row">
@@ -203,15 +171,15 @@ <h2 data-toc-skip>Developers</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/main/katex-auto.js b/main/katex-auto.js
new file mode 100644
index 00000000..20651d9f
--- /dev/null
+++ b/main/katex-auto.js
@@ -0,0 +1,14 @@
+// https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345
+document.addEventListener("DOMContentLoaded", function () {
+  var mathElements = document.getElementsByClassName("math");
+  var macros = [];
+  for (var i = 0; i < mathElements.length; i++) {
+    var texText = mathElements[i].firstChild;
+    if (mathElements[i].tagName == "SPAN") {
+      katex.render(texText.data, mathElements[i], {
+        displayMode: mathElements[i].classList.contains("display"),
+        throwOnError: false,
+        macros: macros,
+        fleqn: false
+      });
+    }}});
diff --git a/main/lightswitch.js b/main/lightswitch.js
new file mode 100644
index 00000000..9467125a
--- /dev/null
+++ b/main/lightswitch.js
@@ -0,0 +1,85 @@
+
+/*!
+ * Color mode toggler for Bootstrap's docs (https://getbootstrap.com/)
+ * Copyright 2011-2023 The Bootstrap Authors
+ * Licensed under the Creative Commons Attribution 3.0 Unported License.
+ * Updates for {pkgdown} by the {bslib} authors, also licensed under CC-BY-3.0.
+ */
+
+const getStoredTheme = () => localStorage.getItem('theme')
+const setStoredTheme = theme => localStorage.setItem('theme', theme)
+
+const getPreferredTheme = () => {
+  const storedTheme = getStoredTheme()
+  if (storedTheme) {
+    return storedTheme
+  }
+
+  return window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light'
+}
+
+const setTheme = theme => {
+  if (theme === 'auto') {
+    document.documentElement.setAttribute('data-bs-theme', (window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light'))
+  } else {
+    document.documentElement.setAttribute('data-bs-theme', theme)
+  }
+}
+
+function bsSetupThemeToggle () {
+  'use strict'
+
+  const showActiveTheme = (theme, focus = false) => {
+    var activeLabel, activeIcon;
+
+    document.querySelectorAll('[data-bs-theme-value]').forEach(element => {
+      const buttonTheme = element.getAttribute('data-bs-theme-value')
+      const isActive = buttonTheme == theme
+      
+      element.classList.toggle('active', isActive)
+      element.setAttribute('aria-pressed', isActive)
+
+      if (isActive) {
+        activeLabel = element.textContent;
+        activeIcon = element.querySelector('span').classList.value;
+      }
+    })
+
+    const themeSwitcher = document.querySelector('#dropdown-lightswitch')
+    if (!themeSwitcher) {
+      return
+    }
+
+    themeSwitcher.setAttribute('aria-label', activeLabel)
+    themeSwitcher.querySelector('span').classList.value = activeIcon;
+
+    if (focus) {
+      themeSwitcher.focus()
+    }
+  }
+
+  window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', () => {
+    const storedTheme = getStoredTheme()
+    if (storedTheme !== 'light' && storedTheme !== 'dark') {
+      setTheme(getPreferredTheme())
+    }
+  })
+
+  window.addEventListener('DOMContentLoaded', () => {
+    showActiveTheme(getPreferredTheme())
+
+    document
+      .querySelectorAll('[data-bs-theme-value]')
+      .forEach(toggle => {
+        toggle.addEventListener('click', () => {
+          const theme = toggle.getAttribute('data-bs-theme-value')
+          setTheme(theme)
+          setStoredTheme(theme)
+          showActiveTheme(theme, true)
+        })
+      })
+  })
+}
+
+setTheme(getPreferredTheme());
+bsSetupThemeToggle();
diff --git a/main/news/index.html b/main/news/index.html
index a88c2cb3..ca036b55 100644
--- a/main/news/index.html
+++ b/main/news/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,61 +7,39 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-news">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Changelog</h1>
-      <small>Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
+      <small>Source: <a href="https://github.com/insightsengineering/hermes/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.7.2.9000" id="hermes-1729000">hermes 1.7.2.9000<a class="anchor" aria-label="anchor" href="#hermes-1729000"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.7.2.9003" id="hermes-1729003">hermes 1.7.2.9003<a class="anchor" aria-label="anchor" href="#hermes-1729003"></a></h2>
 <div class="section level4">
-<h4 id="miscellaneous-1-7-2-9000">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-1-7-2-9000"></a></h4>
+<h4 id="miscellaneous-1-7-2-9003">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-1-7-2-9003"></a></h4>
 <ul><li>Changed maintainer email address.</li>
 </ul></div>
 </div>
@@ -163,7 +138,7 @@ <h4 id="new-features-0-1-0">New Features<a class="anchor" aria-label="anchor" hr
 <li>Perform differential expression analysis.</li>
 </ul></div>
 </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -172,14 +147,14 @@ <h4 id="new-features-0-1-0">New Features<a class="anchor" aria-label="anchor" hr
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/pkgdown.js b/main/pkgdown.js
index 9bd6621e..1a99c65f 100644
--- a/main/pkgdown.js
+++ b/main/pkgdown.js
@@ -153,4 +153,10 @@ async function searchFuse(query, callback) {
   });
 })(window.jQuery || window.$)
 
-
+document.addEventListener('keydown', function(event) {
+  // Check if the pressed key is '/'
+  if (event.key === '/') {
+    event.preventDefault();  // Prevent any default action associated with the '/' key
+    document.getElementById('search-input').focus();  // Set focus to the search input
+  }
+});
diff --git a/main/pkgdown.yml b/main/pkgdown.yml
index e2cd275a..3391cd90 100644
--- a/main/pkgdown.yml
+++ b/main/pkgdown.yml
@@ -1,10 +1,9 @@
-pandoc: '3.2'
-pkgdown: 2.0.9
+pandoc: '3.4'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   hermes: hermes.html
-last_built: 2024-07-16T16:23Z
+last_built: 2024-12-12T14:39Z
 urls:
   reference: https://insightsengineering.github.io/hermes/reference
   article: https://insightsengineering.github.io/hermes/articles
-
diff --git a/main/reference/.ConnectionBiomart.html b/main/reference/.ConnectionBiomart.html
new file mode 100644
index 00000000..1b9404a6
--- /dev/null
+++ b/main/reference/.ConnectionBiomart.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/connect_biomart.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/connect_biomart.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesData.html b/main/reference/.HermesData.html
new file mode 100644
index 00000000..e2a5692e
--- /dev/null
+++ b/main/reference/.HermesData.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataCor.html b/main/reference/.HermesDataCor.html
new file mode 100644
index 00000000..8d3b2220
--- /dev/null
+++ b/main/reference/.HermesDataCor.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_cor.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_cor.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataDiffExpr.html b/main/reference/.HermesDataDiffExpr.html
new file mode 100644
index 00000000..dbba35d9
--- /dev/null
+++ b/main/reference/.HermesDataDiffExpr.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/diff_expression.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/diff_expression.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataPca.html b/main/reference/.HermesDataPca.html
new file mode 100644
index 00000000..88bfe410
--- /dev/null
+++ b/main/reference/.HermesDataPca.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_pca.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_pca.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataPcaCor.html b/main/reference/.HermesDataPcaCor.html
new file mode 100644
index 00000000..bc9368bc
--- /dev/null
+++ b/main/reference/.HermesDataPcaCor.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataSummary.html b/main/reference/.HermesDataSummary.html
new file mode 100644
index 00000000..95206edb
--- /dev/null
+++ b/main/reference/.HermesDataSummary.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/summary.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/summary.html">
+  </head>
+</html>
+
diff --git a/main/reference/.HermesDataTopGenes.html b/main/reference/.HermesDataTopGenes.html
new file mode 100644
index 00000000..38aa4a07
--- /dev/null
+++ b/main/reference/.HermesDataTopGenes.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/top_genes.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/top_genes.html">
+  </head>
+</html>
+
diff --git a/main/reference/.RangedHermesData.html b/main/reference/.RangedHermesData.html
new file mode 100644
index 00000000..e2a5692e
--- /dev/null
+++ b/main/reference/.RangedHermesData.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/.row_data_annotation_cols.html b/main/reference/.row_data_annotation_cols.html
new file mode 100644
index 00000000..52e0445a
--- /dev/null
+++ b/main/reference/.row_data_annotation_cols.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/annotation.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/annotation.html">
+  </head>
+</html>
+
diff --git a/main/reference/AnyHermesData-class.html b/main/reference/AnyHermesData-class.html
new file mode 100644
index 00000000..e2a5692e
--- /dev/null
+++ b/main/reference/AnyHermesData-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/AnyHermesData.html b/main/reference/AnyHermesData.html
new file mode 100644
index 00000000..e2a5692e
--- /dev/null
+++ b/main/reference/AnyHermesData.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/ConnectionBiomart-class.html b/main/reference/ConnectionBiomart-class.html
new file mode 100644
index 00000000..1b9404a6
--- /dev/null
+++ b/main/reference/ConnectionBiomart-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/connect_biomart.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/connect_biomart.html">
+  </head>
+</html>
+
diff --git a/main/reference/ConnectionBiomart.html b/main/reference/ConnectionBiomart.html
new file mode 100644
index 00000000..1b9404a6
--- /dev/null
+++ b/main/reference/ConnectionBiomart.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/connect_biomart.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/connect_biomart.html">
+  </head>
+</html>
+
diff --git a/main/reference/GeneSpec.html b/main/reference/GeneSpec.html
index 6e275c87..e4fc2c28 100644
--- a/main/reference/GeneSpec.html
+++ b/main/reference/GeneSpec.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 Class Representing a Gene (Signature) Specification — GeneSpec • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 Class Representing a Gene (Signature) Specification — GeneSpec"><meta name="description" content="
 A GeneSpec consists of the gene IDs (possibly named with labels),
-the summary function and the name of the summary function."><title>R6 Class Representing a Gene (Signature) Specification — GeneSpec • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 Class Representing a Gene (Signature) Specification — GeneSpec"><meta property="og:description" content="
+the summary function and the name of the summary function."><meta property="og:description" content="
 A GeneSpec consists of the gene IDs (possibly named with labels),
-the summary function and the name of the summary function."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+the summary function and the name of the summary function."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>R6 Class Representing a Gene (Signature) Specification</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
       <div class="d-none name"><code>GeneSpec.Rd</code></div>
     </div>
 
@@ -75,7 +50,7 @@
 
     <div class="section level2">
     <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-    
+
 <div class="section">
 <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
 
@@ -275,7 +250,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5 11         7</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -284,14 +259,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
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-  
 
-  
+
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   </body></html>
 
diff --git a/main/reference/HermesData-class.html b/main/reference/HermesData-class.html
index 8d7c7b32..df5a045e 100644
--- a/main/reference/HermesData-class.html
+++ b/main/reference/HermesData-class.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>HermesData and RangedHermesData — HermesData-class • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="HermesData and RangedHermesData — HermesData-class"><meta name="description" content="
 The HermesData class is an extension of SummarizedExperiment::SummarizedExperiment
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+with additional validation criteria."><meta property="og:description" content="
 The HermesData class is an extension of SummarizedExperiment::SummarizedExperiment
-with additional validation criteria."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
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       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>HermesData</code> and <code>RangedHermesData</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-class.R" class="external-link"><code>R/HermesData-class.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-class.R" class="external-link"><code>R/HermesData-class.R</code></a></small>
       <div class="d-none name"><code>HermesData-class.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental" class="external-link"><img src="figures/lifecycle-experimental.svg" alt="[Experimental]"></a></p>
-<p>The <code>HermesData</code> class is an extension of <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
+<p>The <code>HermesData</code> class is an extension of <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
 with additional validation criteria.</p>
     </div>
 
@@ -81,27 +56,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>SummarizedExperiment</code>)<br> input to create the <code>HermesData</code> object from.
 If this is a <code>RangedSummarizedExperiment</code>, then the result will be
 <code>RangedHermesData</code>.</p></dd>
 
 
-<dt>counts</dt>
+<dt id="arg-counts">counts<a class="anchor" aria-label="anchor" href="#arg-counts"></a></dt>
 <dd><p>(<code>matrix</code>)<br> counts to create the <code>HermesData</code> object from.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments, e.g. <code>rowData</code>, <code>colData</code>, etc. passed to
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment()</a></code> internally. Note that if <code>rowRanges</code>
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment()</a></code> internally. Note that if <code>rowRanges</code>
 is passed instead of <code>rowData</code>, then the result will be a <code>RangedHermesData</code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>An object of class <code>AnyHermesData</code> (<code>HermesData</code> or <code>RangedHermesData</code>).</p>
+    <p>An object of class <code>AnyHermesData</code> (<code>HermesData</code> or <code>RangedHermesData</code>).</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -124,12 +99,12 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 same time with the <code>AnyHermesData</code> signature.</p>
 <p>A <code><a href="https://rdrr.io/pkg/Biobase/man/class.ExpressionSet.html" class="external-link">Biobase::ExpressionSet</a></code> object can be imported by using the
 <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.html" class="external-link">SummarizedExperiment::makeSummarizedExperimentFromExpressionSet()</a></code> function to
-first convert it to a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object before
+first convert it to a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object before
 converting it again into a <code>HermesData</code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2>
-    
+
 
 <dl><dt><code>prefix</code></dt>
 <dd><p>common prefix of the gene IDs (row names).</p></dd>
@@ -138,7 +113,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 </dl></div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
-    
+
 <ul><li><p>Note that we use <code><a href="https://rdrr.io/pkg/S4Vectors/man/S4Vectors-internals.html" class="external-link">S4Vectors::setValidity2()</a></code> to define the validity
 method, which allows us to turn off the validity checks in internal
 functions where intermediate objects may not be valid within the scope of
@@ -188,7 +163,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">counts_hermes_data</span> <span class="op">&lt;-</span> <span class="fu">HermesDataFromMatrix</span><span class="op">(</span><span class="va">counts_matrix</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -197,14 +172,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/HermesData.html b/main/reference/HermesData.html
new file mode 100644
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+++ b/main/reference/HermesData.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataCor-class.html b/main/reference/HermesDataCor-class.html
new file mode 100644
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+++ b/main/reference/HermesDataCor-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_cor.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_cor.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataCor.html b/main/reference/HermesDataCor.html
new file mode 100644
index 00000000..8d3b2220
--- /dev/null
+++ b/main/reference/HermesDataCor.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_cor.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_cor.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataDiffExpr-class.html b/main/reference/HermesDataDiffExpr-class.html
new file mode 100644
index 00000000..dbba35d9
--- /dev/null
+++ b/main/reference/HermesDataDiffExpr-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/diff_expression.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/diff_expression.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataDiffExpr.html b/main/reference/HermesDataDiffExpr.html
new file mode 100644
index 00000000..dbba35d9
--- /dev/null
+++ b/main/reference/HermesDataDiffExpr.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/diff_expression.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/diff_expression.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataFromMatrix.html b/main/reference/HermesDataFromMatrix.html
new file mode 100644
index 00000000..e2a5692e
--- /dev/null
+++ b/main/reference/HermesDataFromMatrix.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataPca-class.html b/main/reference/HermesDataPca-class.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/HermesDataPca-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_pca.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_pca.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataPca.html b/main/reference/HermesDataPca.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/HermesDataPca.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_pca.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_pca.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataPcaCor-class.html b/main/reference/HermesDataPcaCor-class.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/HermesDataPcaCor-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataPcaCor.html b/main/reference/HermesDataPcaCor.html
new file mode 100644
index 00000000..bc9368bc
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+++ b/main/reference/HermesDataPcaCor.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataSummary-class.html b/main/reference/HermesDataSummary-class.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/HermesDataSummary-class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/summary.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/summary.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataSummary.html b/main/reference/HermesDataSummary.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/HermesDataSummary.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/summary.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/summary.html">
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diff --git a/main/reference/HermesDataTopGenes-class.html b/main/reference/HermesDataTopGenes-class.html
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+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/top_genes.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/top_genes.html">
+  </head>
+</html>
+
diff --git a/main/reference/HermesDataTopGenes.html b/main/reference/HermesDataTopGenes.html
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+<html>
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+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/top_genes.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/top_genes.html">
+  </head>
+</html>
+
diff --git a/main/reference/RangedHermesData-class.html b/main/reference/RangedHermesData-class.html
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+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/RangedHermesData.html b/main/reference/RangedHermesData.html
new file mode 100644
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+++ b/main/reference/RangedHermesData.html
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+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/HermesData-class.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/HermesData-class.html">
+  </head>
+</html>
+
diff --git a/main/reference/Rplot001.png b/main/reference/Rplot001.png
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diff --git a/main/reference/all_na.html b/main/reference/all_na.html
index d8b5d31d..32378d62 100644
--- a/main/reference/all_na.html
+++ b/main/reference/all_na.html
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 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function to check whether a whole vector is NA."><title>Checks Whether All Missing — all_na • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Checks Whether All Missing — all_na"><meta property="og:description" content="Internal function to check whether a whole vector is NA."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Checks Whether All Missing — all_na • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Checks Whether All Missing — all_na"><meta name="description" content="Internal function to check whether a whole vector is NA."><meta property="og:description" content="Internal function to check whether a whole vector is NA."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -10,55 +7,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     </button>
 
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-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Checks Whether All Missing</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>all_na.Rd</code></div>
     </div>
 
@@ -73,18 +48,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>vector</code>)<br> vector to check.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Corresponding flag.</p>
+    <p>Corresponding flag.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -93,14 +68,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/annotation.html b/main/reference/annotation.html
index a0bb7aea..047cb3b4 100644
--- a/main/reference/annotation.html
+++ b/main/reference/annotation.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-These methods access and set the gene annotations stored in a AnyHermesData object."><title>Annotation Accessor and Setter — annotation,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Annotation Accessor and Setter — annotation,AnyHermesData-method"><meta property="og:description" content="
-These methods access and set the gene annotations stored in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Annotation Accessor and Setter — annotation,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Annotation Accessor and Setter — annotation,AnyHermesData-method"><meta name="description" content="
+These methods access and set the gene annotations stored in a AnyHermesData object."><meta property="og:description" content="
+These methods access and set the gene annotations stored in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Annotation Accessor and Setter</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>annotation.Rd</code></div>
     </div>
 
@@ -71,12 +46,12 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">annotation</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="va">.row_data_annotation_cols</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData,DataFrame</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData,DataFrame'</span></span>
 <span><span class="fu">annotation</span><span class="op">(</span><span class="va">object</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">value</span></span></code></pre></div>
     </div>
 
@@ -87,23 +62,23 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
     </div>
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to access the annotations from.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>not used.</p></dd>
 
 
-<dt>value</dt>
+<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt>
 <dd><p>(<code>DataFrame</code>)<br> what should the annotations be replaced with.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code><a href="https://rdrr.io/pkg/S4Vectors/man/DataFrame-class.html" class="external-link">S4Vectors::DataFrame</a></code> with the gene annotations:</p><ul><li><p><code>symbol</code></p></li>
+    <p>The <code><a href="https://rdrr.io/pkg/S4Vectors/man/DataFrame-class.html" class="external-link">S4Vectors::DataFrame</a></code> with the gene annotations:</p><ul><li><p><code>symbol</code></p></li>
 <li><p><code>desc</code></p></li>
 <li><p><code>chromosome</code></p></li>
 <li><p><code>size</code></p></li>
@@ -132,7 +107,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> GeneID:64881           PCDH20       protocadherin 20          13      5838</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -141,14 +116,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/assert_proportion.html b/main/reference/assert_proportion.html
new file mode 100644
index 00000000..fec621f4
--- /dev/null
+++ b/main/reference/assert_proportion.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/check_proportion.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/check_proportion.html">
+  </head>
+</html>
+
diff --git a/main/reference/assertion_arguments.html b/main/reference/assertion_arguments.html
index 5eb8ef91..2623a926 100644
--- a/main/reference/assertion_arguments.html
+++ b/main/reference/assertion_arguments.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The documentation to this function lists all the conventional arguments in
-additional checkmate assertions."><title>Standard Assertion Arguments — assertion_arguments • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Standard Assertion Arguments — assertion_arguments"><meta property="og:description" content="The documentation to this function lists all the conventional arguments in
-additional checkmate assertions."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Standard Assertion Arguments — assertion_arguments • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Standard Assertion Arguments — assertion_arguments"><meta name="description" content="The documentation to this function lists all the conventional arguments in
+additional checkmate assertions."><meta property="og:description" content="The documentation to this function lists all the conventional arguments in
+additional checkmate assertions."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Standard Assertion Arguments</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/argument_convention.R" class="external-link"><code>R/argument_convention.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/argument_convention.R" class="external-link"><code>R/argument_convention.R</code></a></small>
       <div class="d-none name"><code>assertion_arguments.Rd</code></div>
     </div>
 
@@ -72,30 +47,32 @@
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>an object to check.</p></dd>
 
 
-<dt>null.ok</dt>
+<dt id="arg-null-ok">null.ok<a class="anchor" aria-label="anchor" href="#arg-null-ok"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether <code>x</code> may also be <code>NULL</code>.</p></dd>
 
 
-<dt>.var.name</dt>
+<dt id="arg--var-name">.var.name<a class="anchor" aria-label="anchor" href="#arg--var-name"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the checked object to print in
 assertions; defaults to the heuristic implemented in <code><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">checkmate::vname()</a></code>.</p></dd>
 
 
-<dt>add</dt>
+<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt>
 <dd><p>(<code>AssertCollection</code> or <code>NULL</code>)<br> collection to store
 assertion messages, see <code><a href="https://mllg.github.io/checkmate/reference/AssertCollection.html" class="external-link">checkmate::AssertCollection</a></code>.</p></dd>
 
 
-<dt>info</dt>
+<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
 <dd><p>(<code>string</code>)<br> extra information to be included in the
 message for the <code>testthat</code> reporter, see <code><a href="https://testthat.r-lib.org/reference/expect_that.html" class="external-link">testthat::expect_that()</a></code>.</p></dd>
 
 
-<dt>label</dt>
+<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the checked object to print in
 messages. Defaults to the heuristic implemented in <code><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">checkmate::vname()</a></code>.</p></dd>
 
@@ -109,14 +86,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/assertions.html b/main/reference/assertions.html
index fcef15df..51099c1d 100644
--- a/main/reference/assertions.html
+++ b/main/reference/assertions.html
@@ -1,20 +1,17 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
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 We provide additional assertion functions which can be used together with
 assertthat::assert_that().
 
 We provide additional assertion functions which can be used together with
 the checkmate functions. These are described in individual help pages
-linked below."><title>Additional Assertions for assert_that — assertions • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additional Assertions for assert_that — assertions"><meta property="og:description" content="
+linked below."><meta property="og:description" content="
 We provide additional assertion functions which can be used together with
 assertthat::assert_that().
 
 We provide additional assertion functions which can be used together with
 the checkmate functions. These are described in individual help pages
-linked below."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -22,55 +19,33 @@
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Additional Assertions for <code>assert_that</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/assertthat.R" class="external-link"><code>R/assertthat.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/checkmate.R" class="external-link"><code>R/checkmate.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/assertthat.R" class="external-link"><code>R/assertthat.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/main/R/checkmate.R" class="external-link"><code>R/checkmate.R</code></a></small>
       <div class="d-none name"><code>assertions.Rd</code></div>
     </div>
 
@@ -101,31 +76,31 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>an object to check.</p></dd>
 
 
-<dt>class2</dt>
+<dt id="arg-class-">class2<a class="anchor" aria-label="anchor" href="#arg-class-"></a></dt>
 <dd><p>(<code>character</code> or class definition)<br> the class to which <code>x</code> could belong.</p></dd>
 
 
-<dt>elements</dt>
+<dt id="arg-elements">elements<a class="anchor" aria-label="anchor" href="#arg-elements"></a></dt>
 <dd><p>(<code>character</code>)<br> names of elements which should be in the list <code>x</code>.</p></dd>
 
 
-<dt>one</dt>
+<dt id="arg-one">one<a class="anchor" aria-label="anchor" href="#arg-one"></a></dt>
 <dd><p>first input.</p></dd>
 
 
-<dt>two</dt>
+<dt id="arg-two">two<a class="anchor" aria-label="anchor" href="#arg-two"></a></dt>
 <dd><p>second input.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Depending on the function prefix.</p><ul><li><p><code>assert_</code> functions return the object invisibly if successful, and otherwise
+    <p>Depending on the function prefix.</p><ul><li><p><code>assert_</code> functions return the object invisibly if successful, and otherwise
 throw an error message.</p></li>
 <li><p><code>check_</code> functions return <code>TRUE</code> if successful, otherwise a string with the
 error message.</p></li>
@@ -133,7 +108,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </ul></div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>is_class()</code>: checks the class.</p></li>
 <li><p><code>is_hermes_data()</code>: checks whether <code>x</code> is an <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p></li>
 <li><p><code>is_counts_vector()</code>: checks for a vector of counts (positive integers).</p></li>
@@ -191,7 +166,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -200,14 +175,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/autoplot,HermesDataCor-method.html b/main/reference/autoplot,HermesDataCor-method.html
new file mode 100644
index 00000000..8d3b2220
--- /dev/null
+++ b/main/reference/autoplot,HermesDataCor-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/calc_cor.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/calc_cor.html">
+  </head>
+</html>
+
diff --git a/main/reference/autoplot,HermesDataDiffExpr-method.html b/main/reference/autoplot,HermesDataDiffExpr-method.html
new file mode 100644
index 00000000..dbba35d9
--- /dev/null
+++ b/main/reference/autoplot,HermesDataDiffExpr-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/diff_expression.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/diff_expression.html">
+  </head>
+</html>
+
diff --git a/main/reference/autoplot,HermesDataPcaCor-method.html b/main/reference/autoplot,HermesDataPcaCor-method.html
new file mode 100644
index 00000000..bc9368bc
--- /dev/null
+++ b/main/reference/autoplot,HermesDataPcaCor-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html">
+  </head>
+</html>
+
diff --git a/main/reference/autoplot,HermesDataTopGenes-method.html b/main/reference/autoplot,HermesDataTopGenes-method.html
new file mode 100644
index 00000000..38aa4a07
--- /dev/null
+++ b/main/reference/autoplot,HermesDataTopGenes-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/top_genes.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/top_genes.html">
+  </head>
+</html>
+
diff --git a/main/reference/calc_cor.html b/main/reference/calc_cor.html
index ad94e41e..6130977d 100644
--- a/main/reference/calc_cor.html
+++ b/main/reference/calc_cor.html
@@ -1,20 +1,17 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method"><meta name="description" content="
 The correlate() method can calculate the correlation matrix between the sample vectors of
 counts from a specified assay. This produces a HermesDataCor object, which is an extension
 of a matrix with additional quality flags in the slot flag_data
 (containing the tech_failure_flag and low_depth_flag columns describing the original
 input samples).
-An autoplot() method then afterwards can produce the corresponding heatmap."><title>Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method"><meta property="og:description" content="
+An autoplot() method then afterwards can produce the corresponding heatmap."><meta property="og:description" content="
 The correlate() method can calculate the correlation matrix between the sample vectors of
 counts from a specified assay. This produces a HermesDataCor object, which is an extension
 of a matrix with additional quality flags in the slot flag_data
 (containing the tech_failure_flag and low_depth_flag columns describing the original
 input samples).
-An autoplot() method then afterwards can produce the corresponding heatmap."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+An autoplot() method then afterwards can produce the corresponding heatmap."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -22,55 +19,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Correlation between Sample Counts of <code>AnyHermesData</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/calc_cor.R" class="external-link"><code>R/calc_cor.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/calc_cor.R" class="external-link"><code>R/calc_cor.R</code></a></small>
       <div class="d-none name"><code>calc_cor.Rd</code></div>
     </div>
 
@@ -86,10 +61,10 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu"><a href="correlate.html">correlate</a></span><span class="op">(</span><span class="va">object</span>, assay_name <span class="op">=</span> <span class="st">"counts"</span>, method <span class="op">=</span> <span class="st">"pearson"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for HermesDataCor</span></span>
+<span><span class="co"># S4 method for class 'HermesDataCor'</span></span>
 <span><span class="fu">autoplot</span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  flag_colors <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>`FALSE` <span class="op">=</span> <span class="st">"green"</span>, `TRUE` <span class="op">=</span> <span class="st">"red"</span><span class="op">)</span>,</span>
@@ -100,41 +75,41 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to calculate the correlation.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> the name of the assay to use.</p></dd>
 
 
-<dt>method</dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
 <dd><p>(<code>string</code>)<br> the correlation method, see <code><a href="https://rdrr.io/r/stats/cor.html" class="external-link">stats::cor()</a></code> for details.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other arguments to be passed to <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap()</a></code>.</p></dd>
 
 
-<dt>flag_colors</dt>
+<dt id="arg-flag-colors">flag_colors<a class="anchor" aria-label="anchor" href="#arg-flag-colors"></a></dt>
 <dd><p>(named <code>character</code>)<br> a vector that specifies the colors for <code>TRUE</code> and <code>FALSE</code>
 flag values.</p></dd>
 
 
-<dt>cor_colors</dt>
+<dt id="arg-cor-colors">cor_colors<a class="anchor" aria-label="anchor" href="#arg-cor-colors"></a></dt>
 <dd><p>(<code>function</code>)<br> color scale function for the correlation values in the heatmap,
 produced by <code><a href="https://rdrr.io/pkg/circlize/man/colorRamp2.html" class="external-link">circlize::colorRamp2()</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A <code>HermesDataCor</code> object.</p>
+    <p>A <code>HermesDataCor</code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>autoplot(HermesDataCor)</code>: This <code>autoplot()</code> method uses the <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap()</a></code> function
 to plot the correlations between samples saved in a <code>HermesDataCor</code> object.</p></li>
 </ul></div>
@@ -288,7 +263,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="calc_cor-3.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -297,14 +272,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/calc_pca-1.png b/main/reference/calc_pca-1.png
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diff --git a/main/reference/calc_pca-2.png b/main/reference/calc_pca-2.png
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diff --git a/main/reference/calc_pca-3.png b/main/reference/calc_pca-3.png
index 1858456e..f770f2df 100644
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diff --git a/main/reference/calc_pca-4.png b/main/reference/calc_pca-4.png
index fd85433a..340ffcfd 100644
Binary files a/main/reference/calc_pca-4.png and b/main/reference/calc_pca-4.png differ
diff --git a/main/reference/calc_pca.html b/main/reference/calc_pca.html
index 58401d6a..30d8eada 100644
--- a/main/reference/calc_pca.html
+++ b/main/reference/calc_pca.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Principal Components Analysis Calculation — calc_pca • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Principal Components Analysis Calculation — calc_pca"><meta name="description" content="
 The calc_pca() function performs principal components analysis of the gene count
 vectors across all samples.
-A corresponding autoplot() method then can visualize the results."><title>Principal Components Analysis Calculation — calc_pca • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Principal Components Analysis Calculation — calc_pca"><meta property="og:description" content="
+A corresponding autoplot() method then can visualize the results."><meta property="og:description" content="
 The calc_pca() function performs principal components analysis of the gene count
 vectors across all samples.
-A corresponding autoplot() method then can visualize the results."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+A corresponding autoplot() method then can visualize the results."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Principal Components Analysis Calculation</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/pca.R" class="external-link"><code>R/pca.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/pca.R" class="external-link"><code>R/pca.R</code></a></small>
       <div class="d-none name"><code>calc_pca.Rd</code></div>
     </div>
 
@@ -82,27 +57,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>) <br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>) <br> name of the assay to use.</p></dd>
 
 
-<dt>n_top</dt>
+<dt id="arg-n-top">n_top<a class="anchor" aria-label="anchor" href="#arg-n-top"></a></dt>
 <dd><p>(<code>count</code> or <code>NULL</code>)<br> filter criteria based on number of genes with maximum variance.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A HermesDataPca object which is an extension of the <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">stats::prcomp</a> class.</p>
+    <p>A HermesDataPca object which is an extension of the <a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">stats::prcomp</a> class.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>PCA should be performed after filtering out low quality genes and samples, as well as
 normalization of counts.</p></li>
 <li><p>In addition, genes with constant counts across all samples are excluded from
@@ -168,7 +143,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="calc_pca-4.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -177,14 +152,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/cat_with_newline.html b/main/reference/cat_with_newline.html
index f573205d..6f9b28f9 100644
--- a/main/reference/cat_with_newline.html
+++ b/main/reference/cat_with_newline.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Concatenate and Print with Newline — cat_with_newline • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Concatenate and Print with Newline — cat_with_newline"><meta name="description" content="
 This function concatenates inputs like cat()
-and prints them with newline."><title>Concatenate and Print with Newline — cat_with_newline • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Concatenate and Print with Newline — cat_with_newline"><meta property="og:description" content="
+and prints them with newline."><meta property="og:description" content="
 This function concatenates inputs like cat()
-and prints them with newline."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+and prints them with newline."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Concatenate and Print with Newline</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>cat_with_newline.Rd</code></div>
     </div>
 
@@ -79,15 +54,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>...</dt>
+
+
+<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>inputs to concatenate.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>None, only used for the side effect of producing the concatenated output in the R console.</p>
+    <p>None, only used for the side effect of producing the concatenated output in the R console.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -100,7 +75,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> hello world</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -109,14 +84,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/cbind.html b/main/reference/cbind.html
index 670842aa..54e39b4b 100644
--- a/main/reference/cbind.html
+++ b/main/reference/cbind.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Column Binding of AnyHermesData Objects — cbind • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Column Binding of AnyHermesData Objects — cbind"><meta name="description" content="
 This method combines AnyHermesData objects with the same ranges but different
-samples (columns in assays)."><title>Column Binding of AnyHermesData Objects — cbind • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Column Binding of AnyHermesData Objects — cbind"><meta property="og:description" content="
+samples (columns in assays)."><meta property="og:description" content="
 This method combines AnyHermesData objects with the same ranges but different
-samples (columns in assays)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+samples (columns in assays)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-        <a href="#" class="nav-link dropdown-toggle"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Column Binding of <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>cbind.Rd</code></div>
     </div>
 
@@ -75,24 +50,24 @@
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>...</dt>
+
+
+<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> objects to column bind.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The combined <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
+    <p>The combined <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
-    
+
 <ul><li><p>Note that this just inherits
 <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::cbind,SummarizedExperiment-method()</a></code>. When binding a
-<code><a href="HermesData-class.html">AnyHermesData</a></code> object with a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
+<code><a href="HermesData-class.html">AnyHermesData</a></code> object with a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
 object, then the result will be a
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object (the more general
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object (the more general
 class).</p></li>
 <li><p>Note that the combined object needs to have unique sample IDs (column names).</p></li>
 </ul></div>
@@ -112,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "hermes"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -121,14 +96,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/check_proportion.html b/main/reference/check_proportion.html
index e089d223..e44fb4f2 100644
--- a/main/reference/check_proportion.html
+++ b/main/reference/check_proportion.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-Check whether x is a (single) proportion."><title>Check for proportion — check_proportion • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check for proportion — check_proportion"><meta property="og:description" content="
-Check whether x is a (single) proportion."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Check for proportion — check_proportion • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Check for proportion — check_proportion"><meta name="description" content="
+Check whether x is a (single) proportion."><meta property="og:description" content="
+Check whether x is a (single) proportion."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-<li class="active nav-item">
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Check for proportion</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/checkmate.R" class="external-link"><code>R/checkmate.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/checkmate.R" class="external-link"><code>R/checkmate.R</code></a></small>
       <div class="d-none name"><code>check_proportion.Rd</code></div>
     </div>
 
@@ -87,39 +62,39 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>an object to check.</p></dd>
 
 
-<dt>null.ok</dt>
+<dt id="arg-null-ok">null.ok<a class="anchor" aria-label="anchor" href="#arg-null-ok"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether <code>x</code> may also be <code>NULL</code>.</p></dd>
 
 
-<dt>.var.name</dt>
+<dt id="arg--var-name">.var.name<a class="anchor" aria-label="anchor" href="#arg--var-name"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the checked object to print in
 assertions; defaults to the heuristic implemented in <code><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">checkmate::vname()</a></code>.</p></dd>
 
 
-<dt>add</dt>
+<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt>
 <dd><p>(<code>AssertCollection</code> or <code>NULL</code>)<br> collection to store
 assertion messages, see <code><a href="https://mllg.github.io/checkmate/reference/AssertCollection.html" class="external-link">checkmate::AssertCollection</a></code>.</p></dd>
 
 
-<dt>info</dt>
+<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
 <dd><p>(<code>string</code>)<br> extra information to be included in the
 message for the <code>testthat</code> reporter, see <code><a href="https://testthat.r-lib.org/reference/expect_that.html" class="external-link">testthat::expect_that()</a></code>.</p></dd>
 
 
-<dt>label</dt>
+<dt id="arg-label">label<a class="anchor" aria-label="anchor" href="#arg-label"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the checked object to print in
 messages. Defaults to the heuristic implemented in <code><a href="https://mllg.github.io/checkmate/reference/vname.html" class="external-link">checkmate::vname()</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>TRUE</code> if successful, otherwise a string with the error message.</p>
+    <p><code>TRUE</code> if successful, otherwise a string with the error message.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -132,7 +107,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -141,14 +116,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/colMeanZscores.html b/main/reference/colMeanZscores.html
index ede98e86..036e6b6c 100644
--- a/main/reference/colMeanZscores.html
+++ b/main/reference/colMeanZscores.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This helper function returns the Z-score from an assay stored as a matrix."><title>Mean Z-score Gene Signature — colMeanZscores • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean Z-score Gene Signature — colMeanZscores"><meta property="og:description" content="
-This helper function returns the Z-score from an assay stored as a matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Mean Z-score Gene Signature — colMeanZscores • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean Z-score Gene Signature — colMeanZscores"><meta name="description" content="
+This helper function returns the Z-score from an assay stored as a matrix."><meta property="og:description" content="
+This helper function returns the Z-score from an assay stored as a matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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       </ul></div>
 
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Mean Z-score Gene Signature</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>colMeanZscores.Rd</code></div>
     </div>
 
@@ -76,16 +51,16 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>matrix</code>)<br> containing numeric data with genes in rows and samples
 in columns, no missing values are allowed.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A numeric vector containing the mean Z-score values for each
+    <p>A numeric vector containing the mean Z-score values for each
 column in <code>x</code>.</p>
     </div>
 
@@ -108,7 +83,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>  -5.682047e-04   7.648360e-04   2.441182e-04   8.012106e-04 </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -117,14 +92,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/main/reference/colPrinComp1.html b/main/reference/colPrinComp1.html
index aed27d29..9c36596c 100644
--- a/main/reference/colPrinComp1.html
+++ b/main/reference/colPrinComp1.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>First Principal Component (PC1) Gene Signature — colPrinComp1 • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="First Principal Component (PC1) Gene Signature — colPrinComp1"><meta name="description" content="
 This helper function returns the first principal component from an assay
-stored as a matrix."><title>First Principal Component (PC1) Gene Signature — colPrinComp1 • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="First Principal Component (PC1) Gene Signature — colPrinComp1"><meta property="og:description" content="
+stored as a matrix."><meta property="og:description" content="
 This helper function returns the first principal component from an assay
-stored as a matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
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 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>First Principal Component (PC1) Gene Signature</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>colPrinComp1.Rd</code></div>
     </div>
 
@@ -79,24 +54,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>matrix</code>)<br> containing numeric data with genes in rows and samples
 in columns, no missing values are allowed.</p></dd>
 
 
-<dt>center</dt>
+<dt id="arg-center">center<a class="anchor" aria-label="anchor" href="#arg-center"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether the variables should be zero centered.</p></dd>
 
 
-<dt>scale</dt>
+<dt id="arg-scale">scale<a class="anchor" aria-label="anchor" href="#arg-scale"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether the variables should be scaled to have unit variance.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A numeric vector containing the principal component values for each
+    <p>A numeric vector containing the principal component values for each
 column in <code>x</code>.</p>
     </div>
 
@@ -119,7 +94,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>     -5.3048871     32.7696234      9.9885728      4.3472814 </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -128,14 +103,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/col_data_with_genes.html b/main/reference/col_data_with_genes.html
index 17c1823a..a3cc257f 100644
--- a/main/reference/col_data_with_genes.html
+++ b/main/reference/col_data_with_genes.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Sample Variables with Selected Gene Information — col_data_with_genes • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample Variables with Selected Gene Information — col_data_with_genes"><meta name="description" content="
 This obtains the sample variables of a HermesData object together
-with selected gene information."><title>Sample Variables with Selected Gene Information — col_data_with_genes • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample Variables with Selected Gene Information — col_data_with_genes"><meta property="og:description" content="
+with selected gene information."><meta property="og:description" content="
 This obtains the sample variables of a HermesData object together
-with selected gene information."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+with selected gene information."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Sample Variables with Selected Gene Information</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/join_cdisc.R" class="external-link"><code>R/join_cdisc.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/join_cdisc.R" class="external-link"><code>R/join_cdisc.R</code></a></small>
       <div class="d-none name"><code>col_data_with_genes.Rd</code></div>
     </div>
 
@@ -79,23 +54,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input experiment.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> which assay to use.</p></dd>
 
 
-<dt>genes</dt>
+<dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> which genes or which gene signature should be extracted.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The combined data set, where the additional attribute <code>gene_cols</code> contains
+    <p>The combined data set, where the additional attribute <code>gene_cols</code> contains
 the names of the columns obtained by extracting the <code>genes</code> information.</p>
     </div>
     <div class="section level2">
@@ -115,7 +90,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [20] 161</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -124,14 +99,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/connect_biomart.html b/main/reference/connect_biomart.html
index 45f461be..23b1f4b7 100644
--- a/main/reference/connect_biomart.html
+++ b/main/reference/connect_biomart.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Connection to BioMart — connect_biomart • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Connection to BioMart — connect_biomart"><meta name="description" content="
 connect_biomart() creates a connection object of class ConnectionBiomart which contains
 the biomaRt object of class biomaRt::Mart and the prefix of the object
-which is used downstream for the query."><title>Connection to BioMart — connect_biomart • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Connection to BioMart — connect_biomart"><meta property="og:description" content="
+which is used downstream for the query."><meta property="og:description" content="
 connect_biomart() creates a connection object of class ConnectionBiomart which contains
 the biomaRt object of class biomaRt::Mart and the prefix of the object
-which is used downstream for the query."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+which is used downstream for the query."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Connection to <code>BioMart</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>connect_biomart.Rd</code></div>
     </div>
 
@@ -82,20 +57,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>prefix</dt>
+
+
+<dl><dt id="arg-prefix">prefix<a class="anchor" aria-label="anchor" href="#arg-prefix"></a></dt>
 <dd><p>(<code>string</code>)<br> gene ID prefix.</p></dd>
 
 
-<dt>version</dt>
+<dt id="arg-version">version<a class="anchor" aria-label="anchor" href="#arg-version"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional <code>Ensembl</code> version to use. If <code>NULL</code>
 the latest available release is used.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>ConnectionBiomart</code> object.</p>
+    <p><code>ConnectionBiomart</code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -111,7 +86,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -120,14 +95,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/control_normalize.html b/main/reference/control_normalize.html
index f37bc1f1..9484d3bc 100644
--- a/main/reference/control_normalize.html
+++ b/main/reference/control_normalize.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This control function allows for easy customization of the normalization settings."><title>Control Settings for Counts Normalization — control_normalize • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control Settings for Counts Normalization — control_normalize"><meta property="og:description" content="
-This control function allows for easy customization of the normalization settings."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control Settings for Counts Normalization — control_normalize • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control Settings for Counts Normalization — control_normalize"><meta name="description" content="
+This control function allows for easy customization of the normalization settings."><meta property="og:description" content="
+This control function allows for easy customization of the normalization settings."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Control Settings for Counts Normalization</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/normalization.R" class="external-link"><code>R/normalization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/normalization.R" class="external-link"><code>R/normalization.R</code></a></small>
       <div class="d-none name"><code>control_normalize.Rd</code></div>
     </div>
 
@@ -81,21 +56,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>log</dt>
+
+
+<dl><dt id="arg-log">log<a class="anchor" aria-label="anchor" href="#arg-log"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether <code>log2</code> values are returned, otherwise original scale is used.</p></dd>
 
 
-<dt>lib_sizes</dt>
+<dt id="arg-lib-sizes">lib_sizes<a class="anchor" aria-label="anchor" href="#arg-lib-sizes"></a></dt>
 <dd><p>(<code>NULL</code> or <code>counts</code>)<br> library sizes, if <code>NULL</code> the vector with the sum of the
 counts for each of the samples will be used.</p></dd>
 
 
-<dt>prior_count</dt>
+<dt id="arg-prior-count">prior_count<a class="anchor" aria-label="anchor" href="#arg-prior-count"></a></dt>
 <dd><p>(non-negative <code>number</code>)<br> average count to be added to each observation to
 avoid taking log of zero, used only when <code>log = TRUE</code>.</p></dd>
 
 
-<dt>fit_type</dt>
+<dt id="arg-fit-type">fit_type<a class="anchor" aria-label="anchor" href="#arg-fit-type"></a></dt>
 <dd><p>(<code>string</code>)<br> method to estimate dispersion parameters
 in Negative Binomial model, used only when <code><a href="normalize.html">normalize()</a></code> methods include <code>vst</code> and/or <code>rlog</code>.
 See <code>estimateDispersions</code> for details.</p></dd>
@@ -103,9 +80,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List with the above settings used to perform the normalization procedure.</p>
+    <p>List with the above settings used to perform the normalization procedure.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -144,7 +119,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -153,14 +128,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/control_quality.html b/main/reference/control_quality.html
index d282932b..453fbfad 100644
--- a/main/reference/control_quality.html
+++ b/main/reference/control_quality.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Control for Specified Quality Flags — control_quality • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control for Specified Quality Flags — control_quality"><meta name="description" content="
 Control function which specifies the quality flag settings.
-One or more settings can be customized. Not specified settings are left at defaults."><title>Control for Specified Quality Flags — control_quality • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Control for Specified Quality Flags — control_quality"><meta property="og:description" content="
+One or more settings can be customized. Not specified settings are left at defaults."><meta property="og:description" content="
 Control function which specifies the quality flag settings.
-One or more settings can be customized. Not specified settings are left at defaults."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+One or more settings can be customized. Not specified settings are left at defaults."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Control for Specified Quality Flags</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
       <div class="d-none name"><code>control_quality.Rd</code></div>
     </div>
 
@@ -84,22 +59,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>min_cpm</dt>
+
+
+<dl><dt id="arg-min-cpm">min_cpm<a class="anchor" aria-label="anchor" href="#arg-min-cpm"></a></dt>
 <dd><p>(non-negative <code>number</code>)<br> minimum Counts per Million (<code>CPM</code>) for
 each gene within the sample.</p></dd>
 
 
-<dt>min_cpm_prop</dt>
+<dt id="arg-min-cpm-prop">min_cpm_prop<a class="anchor" aria-label="anchor" href="#arg-min-cpm-prop"></a></dt>
 <dd><p>(<code>proportion</code>)<br> minimum proportion of samples with
 acceptable <code>CPM</code> of certain gene for low expression flagging.</p></dd>
 
 
-<dt>min_corr</dt>
+<dt id="arg-min-corr">min_corr<a class="anchor" aria-label="anchor" href="#arg-min-corr"></a></dt>
 <dd><p>(<code>proportion</code>)<br> minimum Pearson correlation coefficient of
 <code>CPM</code> between samples for technical failure flagging.</p></dd>
 
 
-<dt>min_depth</dt>
+<dt id="arg-min-depth">min_depth<a class="anchor" aria-label="anchor" href="#arg-min-depth"></a></dt>
 <dd><p>(non-negative <code>count</code> or <code>NULL</code>)<br> minimum library depth
 for low depth flagging. If <code>NULL</code>, this will be calculated as the first
 quartile minus 1.5 times the inter-quartile range of the library size
@@ -109,9 +86,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List with the above criteria to flag observations.</p>
+    <p>List with the above criteria to flag observations.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -151,7 +126,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -160,14 +135,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/correlate.html b/main/reference/correlate.html
index 9b711902..f2ce52c9 100644
--- a/main/reference/correlate.html
+++ b/main/reference/correlate.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-New generic function to calculate correlations for one or two objects."><title>Generic Function for Correlation Calculations — correlate • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generic Function for Correlation Calculations — correlate"><meta property="og:description" content="
-New generic function to calculate correlations for one or two objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Generic Function for Correlation Calculations — correlate • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generic Function for Correlation Calculations — correlate"><meta name="description" content="
+New generic function to calculate correlations for one or two objects."><meta property="og:description" content="
+New generic function to calculate correlations for one or two objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Generic Function for Correlation Calculations</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>correlate.Rd</code></div>
     </div>
 
@@ -76,19 +51,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>input of which the class will be used to decide the method.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Corresponding object that contains the correlation results.</p>
+    <p>Corresponding object that contains the correlation results.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -106,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="correlate-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -115,14 +90,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/counts.html b/main/reference/counts.html
index d2fceb88..0372eda3 100644
--- a/main/reference/counts.html
+++ b/main/reference/counts.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-These methods access and set the counts assay in a AnyHermesData object."><title>Counts Accessor and Setter — counts,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Counts Accessor and Setter — counts,AnyHermesData-method"><meta property="og:description" content="
-These methods access and set the counts assay in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Counts Accessor and Setter — counts,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Counts Accessor and Setter — counts,AnyHermesData-method"><meta name="description" content="
+These methods access and set the counts assay in a AnyHermesData object."><meta property="og:description" content="
+These methods access and set the counts assay in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Counts Accessor and Setter</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>counts.Rd</code></div>
     </div>
 
@@ -71,24 +46,26 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">counts</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData,matrix</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData,matrix'</span></span>
 <span><span class="fu">counts</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, withDimnames <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">value</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to access the counts from.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>not used.</p></dd>
 
 
-<dt>withDimnames</dt>
+<dt id="arg-withdimnames">withDimnames<a class="anchor" aria-label="anchor" href="#arg-withdimnames"></a></dt>
 <dd><p>(<code>flag</code>)<br> setting <code>withDimnames =FALSE</code> in the setter
 (<code>counts&lt;-</code>) is required when the <code>dimnames</code> on the supplied counts assay
 are not identical to the <code>dimnames</code> on the <code>AnyHermesData</code> object;
@@ -96,19 +73,17 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 (they're always stored as-is).</p></dd>
 
 
-<dt>value</dt>
+<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt>
 <dd><p>(<code>matrix</code>)<br> what should the counts assay be replaced with.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The counts assay.</p>
+    <p>The counts assay.</p>
     </div>
     <div class="section level2">
     <h2 id="methods-by-class-">Methods (by class)<a class="anchor" aria-label="anchor" href="#methods-by-class-"></a></h2>
-    
+
 <ul><li><p><code>counts(object = AnyHermesData) &lt;- value</code>:</p></li>
 </ul></div>
 
@@ -193,7 +168,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> GeneID:64881               1415            100           3147            235</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -202,14 +177,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/cut_quantile.html b/main/reference/cut_quantile.html
index 4f6ba7eb..e9f0dce3 100644
--- a/main/reference/cut_quantile.html
+++ b/main/reference/cut_quantile.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile"><meta name="description" content="
 This function transforms a numeric vector into a factor corresponding to the quantile intervals.
-The intervals are left-open and right-closed."><title>Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile"><meta property="og:description" content="
+The intervals are left-open and right-closed."><meta property="og:description" content="
 This function transforms a numeric vector into a factor corresponding to the quantile intervals.
-The intervals are left-open and right-closed."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+The intervals are left-open and right-closed."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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 </script></head><body>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
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-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Cutting a Numeric Vector into a Factor of Quantile Bins</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>cut_quantile.Rd</code></div>
     </div>
 
@@ -79,25 +54,25 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>numeric</code>)<br> the continuous variable values which should be cut into quantile bins. <code>NA</code> values are
 not taken into account when computing quantiles and are attributed to the <code>NA</code> interval.</p></dd>
 
 
-<dt>percentiles</dt>
+<dt id="arg-percentiles">percentiles<a class="anchor" aria-label="anchor" href="#arg-percentiles"></a></dt>
 <dd><p>(<code>proportions</code>)<br> the required percentiles for the quantile intervals
 to be generated. Duplicated values are removed.</p></dd>
 
 
-<dt>digits</dt>
+<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
 <dd><p>(<code>integer</code>)<br>  the precision to use when formatting the percentages.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The factor with a description of the available quantiles as levels.</p>
+    <p>The factor with a description of the available quantiles as levels.</p>
     </div>
 
     <div class="section level2">
@@ -118,7 +93,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: [0%,33%] (33%,67%] (67%,100%]</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -127,14 +102,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/df_cols_to_factor.html b/main/reference/df_cols_to_factor.html
index 179f6d0a..2d0c7e6d 100644
--- a/main/reference/df_cols_to_factor.html
+++ b/main/reference/df_cols_to_factor.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor"><meta name="description" content="
 This utility function converts all eligible character and logical variables in a
 S4Vectors::DataFrame to factor variables. All factor variables get amended
-with an explicit missing level. This includes both NA and empty strings."><title>Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor"><meta property="og:description" content="
+with an explicit missing level. This includes both NA and empty strings."><meta property="og:description" content="
 This utility function converts all eligible character and logical variables in a
 S4Vectors::DataFrame to factor variables. All factor variables get amended
-with an explicit missing level. This includes both NA and empty strings."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Conversion of Eligible Columns to Factor Variables in a <code>DataFrame</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>df_cols_to_factor.Rd</code></div>
     </div>
 
@@ -82,24 +57,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>data</dt>
+
+
+<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
 <dd><p>(<code>DataFrame</code>)<br> input <code><a href="https://rdrr.io/pkg/S4Vectors/man/DataFrame-class.html" class="external-link">S4Vectors::DataFrame</a></code>.</p></dd>
 
 
-<dt>omit_columns</dt>
+<dt id="arg-omit-columns">omit_columns<a class="anchor" aria-label="anchor" href="#arg-omit-columns"></a></dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> which columns should be omitted from
 the possible conversion to factor and explicit missing level application.</p></dd>
 
 
-<dt>na_level</dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
 <dd><p>(<code>string</code>)<br> explicit missing level to be used for factor variables.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The modified data.</p>
+    <p>The modified data.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -120,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -129,14 +104,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/diff_expression-1.png b/main/reference/diff_expression-1.png
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diff --git a/main/reference/diff_expression.html b/main/reference/diff_expression.html
index b7bc7950..11dab6c6 100644
--- a/main/reference/diff_expression.html
+++ b/main/reference/diff_expression.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Differential Expression Analysis — diff_expression • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Differential Expression Analysis — diff_expression"><meta name="description" content="
 The diff_expression() function performs differential expression analysis
 using a method of preference.
-A corresponding autoplot() method is visualizing the results as a volcano plot."><title>Differential Expression Analysis — diff_expression • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Differential Expression Analysis — diff_expression"><meta property="og:description" content="
+A corresponding autoplot() method is visualizing the results as a volcano plot."><meta property="og:description" content="
 The diff_expression() function performs differential expression analysis
 using a method of preference.
-A corresponding autoplot() method is visualizing the results as a volcano plot."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+A corresponding autoplot() method is visualizing the results as a volcano plot."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Differential Expression Analysis</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
       <div class="d-none name"><code>diff_expression.Rd</code></div>
     </div>
 
@@ -79,45 +54,45 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">diff_expression</span><span class="op">(</span><span class="va">object</span>, <span class="va">group</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"voom"</span>, <span class="st">"deseq2"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for HermesDataDiffExpr</span></span>
+<span><span class="co"># S4 method for class 'HermesDataDiffExpr'</span></span>
 <span><span class="fu">autoplot</span><span class="op">(</span><span class="va">object</span>, adj_p_val_thresh <span class="op">=</span> <span class="fl">0.05</span>, log2_fc_thresh <span class="op">=</span> <span class="fl">2.5</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input. Note that this function only uses the
 original counts for analysis, so this does not need to be normalized.</p></dd>
 
 
-<dt>group</dt>
+<dt id="arg-group">group<a class="anchor" aria-label="anchor" href="#arg-group"></a></dt>
 <dd><p>(<code>string</code>)<br> name of factor variable with 2 levels in <code>colData(object)</code>.
 These 2 levels will be compared in the differential expression analysis.</p></dd>
 
 
-<dt>method</dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
 <dd><p>(<code>string</code>)<br> method for differential expression analysis, see details below.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments passed to the helper function associated with the selected method.</p></dd>
 
 
-<dt>adj_p_val_thresh</dt>
+<dt id="arg-adj-p-val-thresh">adj_p_val_thresh<a class="anchor" aria-label="anchor" href="#arg-adj-p-val-thresh"></a></dt>
 <dd><p>(<code>proportion</code>)<br> threshold on the adjusted p-values (y-axis) to
 flag significance.</p></dd>
 
 
-<dt>log2_fc_thresh</dt>
+<dt id="arg-log-fc-thresh">log2_fc_thresh<a class="anchor" aria-label="anchor" href="#arg-log-fc-thresh"></a></dt>
 <dd><p>(<code>number</code>)<br> threshold on the absolute log2 fold-change (x-axis)
 to flag up- or down-regulation of transcription.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A <code>HermesDataDiffExpr</code> object which is a data frame with the following columns for each gene
+    <p>A <code>HermesDataDiffExpr</code> object which is a data frame with the following columns for each gene
 in the <code><a href="HermesData-class.html">HermesData</a></code> object:</p><ul><li><p><code>log2_fc</code> (the estimate of the log2 fold change between the 2 levels of the
 provided factor)</p></li>
 <li><p><code>stat</code> (the test statistic, which one depends on the method used)</p></li>
@@ -131,12 +106,12 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 </ul></div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>autoplot(HermesDataDiffExpr)</code>: generates a volcano plot for a <code>HermesDataDiffExpr</code> object.</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
-    
+
 <ul><li><p>We provide the <code><a href="df_cols_to_factor.html">df_cols_to_factor()</a></code> utility function that makes it easy to convert the
 <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData()</a></code> character and logical variables to factors, so that they can be subsequently
 used as <code>group</code> inputs. See the example.</p></li>
@@ -200,7 +175,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="diff_expression-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -209,14 +184,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
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index 3d804d3e..1f0a19cb 100644
--- a/main/reference/draw_barplot.html
+++ b/main/reference/draw_barplot.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Barplot for Gene Expression Percentiles — draw_barplot • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Barplot for Gene Expression Percentiles — draw_barplot"><meta name="description" content="
 This produces a barplot of the dichotomized gene expression counts into two or three
-categories based on custom defined percentiles."><title>Barplot for Gene Expression Percentiles — draw_barplot • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Barplot for Gene Expression Percentiles — draw_barplot"><meta property="og:description" content="
+categories based on custom defined percentiles."><meta property="og:description" content="
 This produces a barplot of the dichotomized gene expression counts into two or three
-categories based on custom defined percentiles."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+categories based on custom defined percentiles."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Barplot for Gene Expression Percentiles</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/draw_barplot.R" class="external-link"><code>R/draw_barplot.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/draw_barplot.R" class="external-link"><code>R/draw_barplot.R</code></a></small>
       <div class="d-none name"><code>draw_barplot.Rd</code></div>
     </div>
 
@@ -86,38 +61,38 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> selects assay from input.</p></dd>
 
 
-<dt>x_spec</dt>
+<dt id="arg-x-spec">x_spec<a class="anchor" aria-label="anchor" href="#arg-x-spec"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> gene specification for the x-axis.</p></dd>
 
 
-<dt>facet_var</dt>
+<dt id="arg-facet-var">facet_var<a class="anchor" aria-label="anchor" href="#arg-facet-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional faceting variable, taken
 from input sample variables.</p></dd>
 
 
-<dt>fill_var</dt>
+<dt id="arg-fill-var">fill_var<a class="anchor" aria-label="anchor" href="#arg-fill-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional fill variable, taken
 from input sample variables.</p></dd>
 
 
-<dt>percentiles</dt>
+<dt id="arg-percentiles">percentiles<a class="anchor" aria-label="anchor" href="#arg-percentiles"></a></dt>
 <dd><p>(<code>vector</code>)<br> lower and upper percentiles to dichotomize
 the gene counts into two or three categories.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> barplot.</p>
+    <p>The <code>ggplot</code> barplot.</p>
     </div>
 
     <div class="section level2">
@@ -155,7 +130,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_barplot-3.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -164,14 +139,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_boxplot-1.png b/main/reference/draw_boxplot-1.png
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diff --git a/main/reference/draw_boxplot.html b/main/reference/draw_boxplot.html
index 15819955..2d27ac37 100644
--- a/main/reference/draw_boxplot.html
+++ b/main/reference/draw_boxplot.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Boxplot for Gene Expression Values — draw_boxplot • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Boxplot for Gene Expression Values — draw_boxplot"><meta name="description" content="
 This produces boxplots of the gene expression values of a single gene, multiple genes or
-a gene signature."><title>Boxplot for Gene Expression Values — draw_boxplot • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Boxplot for Gene Expression Values — draw_boxplot"><meta property="og:description" content="
+a gene signature."><meta property="og:description" content="
 This produces boxplots of the gene expression values of a single gene, multiple genes or
-a gene signature."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+a gene signature."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Boxplot for Gene Expression Values</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/draw_boxplot.R" class="external-link"><code>R/draw_boxplot.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/draw_boxplot.R" class="external-link"><code>R/draw_boxplot.R</code></a></small>
       <div class="d-none name"><code>draw_boxplot.Rd</code></div>
     </div>
 
@@ -90,50 +65,50 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> selects assay from input for the y-axis.</p></dd>
 
 
-<dt>genes</dt>
+<dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> for which genes or which gene signature to produce boxplots.</p></dd>
 
 
-<dt>x_var</dt>
+<dt id="arg-x-var">x_var<a class="anchor" aria-label="anchor" href="#arg-x-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional stratifying variable for the x-axis,
 taken from input sample variables.</p></dd>
 
 
-<dt>color_var</dt>
+<dt id="arg-color-var">color_var<a class="anchor" aria-label="anchor" href="#arg-color-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional color variable, taken from
 input sample variables.</p></dd>
 
 
-<dt>facet_var</dt>
+<dt id="arg-facet-var">facet_var<a class="anchor" aria-label="anchor" href="#arg-facet-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional faceting variable, taken
 from input sample variables.</p></dd>
 
 
-<dt>violin</dt>
+<dt id="arg-violin">violin<a class="anchor" aria-label="anchor" href="#arg-violin"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether to draw a violin plot instead of a boxplot.</p></dd>
 
 
-<dt>jitter</dt>
+<dt id="arg-jitter">jitter<a class="anchor" aria-label="anchor" href="#arg-jitter"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether to add jittered original data points.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> boxplot.</p>
+    <p>The <code>ggplot</code> boxplot.</p>
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>h_draw_boxplot_df()</code>: Helper function to prepare the data frame required
 for plotting.</p></li>
 </ul></div>
@@ -183,7 +158,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_boxplot-4.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -192,14 +167,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_genes_barplot-1.png b/main/reference/draw_genes_barplot-1.png
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diff --git a/main/reference/draw_genes_barplot-2.png b/main/reference/draw_genes_barplot-2.png
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diff --git a/main/reference/draw_genes_barplot-4.png b/main/reference/draw_genes_barplot-4.png
index 8572ea54..46b67ed7 100644
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diff --git a/main/reference/draw_genes_barplot.html b/main/reference/draw_genes_barplot.html
index d7b4dc72..0f7e5707 100644
--- a/main/reference/draw_genes_barplot.html
+++ b/main/reference/draw_genes_barplot.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This creates a barplot of chromosomes for the AnyHermesData object with the proportions of low expression genes."><title>Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot"><meta property="og:description" content="
-This creates a barplot of chromosomes for the AnyHermesData object with the proportions of low expression genes."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot"><meta name="description" content="
+This creates a barplot of chromosomes for the AnyHermesData object with the proportions of low expression genes."><meta property="og:description" content="
+This creates a barplot of chromosomes for the AnyHermesData object with the proportions of low expression genes."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Stacked Barplot of Low Expression Genes by Chromosome</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>draw_genes_barplot.Rd</code></div>
     </div>
 
@@ -80,23 +55,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>chromosomes</dt>
+<dt id="arg-chromosomes">chromosomes<a class="anchor" aria-label="anchor" href="#arg-chromosomes"></a></dt>
 <dd><p>(<code>character</code>)<br> names of the chromosomes which should be displayed.</p></dd>
 
 
-<dt>include_others</dt>
+<dt id="arg-include-others">include_others<a class="anchor" aria-label="anchor" href="#arg-include-others"></a></dt>
 <dd><p>(<code>flag</code>)<br> option to show the chromosomes not in <code>chromosomes</code> as "Others".</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> object with the histogram.</p>
+    <p>The <code>ggplot</code> object with the histogram.</p>
     </div>
 
     <div class="section level2">
@@ -121,7 +96,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_genes_barplot-4.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -130,14 +105,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_heatmap.html b/main/reference/draw_heatmap.html
index 686e2314..311e0dd8 100644
--- a/main/reference/draw_heatmap.html
+++ b/main/reference/draw_heatmap.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This produces a heatmap of the chosen assay and groups by various sample variables."><title>Heatmap for Gene Expression Counts — draw_heatmap • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Heatmap for Gene Expression Counts — draw_heatmap"><meta property="og:description" content="
-This produces a heatmap of the chosen assay and groups by various sample variables."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Heatmap for Gene Expression Counts — draw_heatmap • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Heatmap for Gene Expression Counts — draw_heatmap"><meta name="description" content="
+This produces a heatmap of the chosen assay and groups by various sample variables."><meta property="og:description" content="
+This produces a heatmap of the chosen assay and groups by various sample variables."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Heatmap for Gene Expression Counts</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/draw_heatmap.R" class="external-link"><code>R/draw_heatmap.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/draw_heatmap.R" class="external-link"><code>R/draw_heatmap.R</code></a></small>
       <div class="d-none name"><code>draw_heatmap.Rd</code></div>
     </div>
 
@@ -82,33 +57,33 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> selects assay from input.</p></dd>
 
 
-<dt>color_extremes</dt>
+<dt id="arg-color-extremes">color_extremes<a class="anchor" aria-label="anchor" href="#arg-color-extremes"></a></dt>
 <dd><p>(<code>numeric</code>)<br> min and max percentiles to inform the color scheme
 of the heatmap as blue and red respectively.</p></dd>
 
 
-<dt>col_data_annotation</dt>
+<dt id="arg-col-data-annotation">col_data_annotation<a class="anchor" aria-label="anchor" href="#arg-col-data-annotation"></a></dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> optional grouping variable(s), taken
 from input sample variables.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments to pass to <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap()</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap</a></code> heatmap</p>
+    <p>The <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap</a></code> heatmap</p>
     </div>
 
     <div class="section level2">
@@ -134,7 +109,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_heatmap-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -143,14 +118,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_libsize_densities-1.png b/main/reference/draw_libsize_densities-1.png
index fe77ce6c..dfb098ca 100644
Binary files a/main/reference/draw_libsize_densities-1.png and b/main/reference/draw_libsize_densities-1.png differ
diff --git a/main/reference/draw_libsize_densities-2.png b/main/reference/draw_libsize_densities-2.png
index 42f82cc3..705ec2ea 100644
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diff --git a/main/reference/draw_libsize_densities.html b/main/reference/draw_libsize_densities.html
index 51421b47..7e3357cb 100644
--- a/main/reference/draw_libsize_densities.html
+++ b/main/reference/draw_libsize_densities.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Density Plot of (Log) Counts Distributions — draw_libsize_densities • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Density Plot of (Log) Counts Distributions — draw_libsize_densities"><meta name="description" content="
 This creates a density plot of the (log) counts distributions of the AnyHermesData object where each line
-on the plot corresponds to a sample."><title>Density Plot of (Log) Counts Distributions — draw_libsize_densities • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Density Plot of (Log) Counts Distributions — draw_libsize_densities"><meta property="og:description" content="
+on the plot corresponds to a sample."><meta property="og:description" content="
 This creates a density plot of the (log) counts distributions of the AnyHermesData object where each line
-on the plot corresponds to a sample."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+on the plot corresponds to a sample."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Density Plot of (Log) Counts Distributions</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>draw_libsize_densities.Rd</code></div>
     </div>
 
@@ -79,19 +54,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>log</dt>
+<dt id="arg-log">log<a class="anchor" aria-label="anchor" href="#arg-log"></a></dt>
 <dd><p>(<code>flag</code>)<br> should the counts be log transformed (log2).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> object with the density plot.</p>
+    <p>The <code>ggplot</code> object with the density plot.</p>
     </div>
 
     <div class="section level2">
@@ -103,7 +78,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_libsize_densities-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +87,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_libsize_hist-1.png b/main/reference/draw_libsize_hist-1.png
index 4f8c530a..191b1126 100644
Binary files a/main/reference/draw_libsize_hist-1.png and b/main/reference/draw_libsize_hist-1.png differ
diff --git a/main/reference/draw_libsize_hist-2.png b/main/reference/draw_libsize_hist-2.png
index 2773f816..f288f3a1 100644
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diff --git a/main/reference/draw_libsize_hist.html b/main/reference/draw_libsize_hist.html
index 7d4c3025..c46d0477 100644
--- a/main/reference/draw_libsize_hist.html
+++ b/main/reference/draw_libsize_hist.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This creates a histogram of the library sizes of the AnyHermesData object."><title>Histogram of Library Sizes — draw_libsize_hist • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Histogram of Library Sizes — draw_libsize_hist"><meta property="og:description" content="
-This creates a histogram of the library sizes of the AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Histogram of Library Sizes — draw_libsize_hist • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Histogram of Library Sizes — draw_libsize_hist"><meta name="description" content="
+This creates a histogram of the library sizes of the AnyHermesData object."><meta property="og:description" content="
+This creates a histogram of the library sizes of the AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Histogram of Library Sizes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>draw_libsize_hist.Rd</code></div>
     </div>
 
@@ -76,23 +51,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>bins</dt>
+<dt id="arg-bins">bins<a class="anchor" aria-label="anchor" href="#arg-bins"></a></dt>
 <dd><p>(<code>count</code>)<br> number of evenly distributed groups desired.</p></dd>
 
 
-<dt>fill</dt>
+<dt id="arg-fill">fill<a class="anchor" aria-label="anchor" href="#arg-fill"></a></dt>
 <dd><p>(<code>string</code>)<br> color of the bars filling.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> object with the histogram.</p>
+    <p>The <code>ggplot</code> object with the histogram.</p>
     </div>
 
     <div class="section level2">
@@ -104,7 +79,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_libsize_hist-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -113,14 +88,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_libsize_qq-1.png b/main/reference/draw_libsize_qq-1.png
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diff --git a/main/reference/draw_libsize_qq-3.png b/main/reference/draw_libsize_qq-3.png
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diff --git a/main/reference/draw_libsize_qq.html b/main/reference/draw_libsize_qq.html
index d6203143..bc0d0230 100644
--- a/main/reference/draw_libsize_qq.html
+++ b/main/reference/draw_libsize_qq.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This creates a Q-Q plot of the library sizes of the AnyHermesData object."><title>Q-Q Plot of Library Sizes — draw_libsize_qq • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Q-Q Plot of Library Sizes — draw_libsize_qq"><meta property="og:description" content="
-This creates a Q-Q plot of the library sizes of the AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Q-Q Plot of Library Sizes — draw_libsize_qq • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Q-Q Plot of Library Sizes — draw_libsize_qq"><meta name="description" content="
+This creates a Q-Q plot of the library sizes of the AnyHermesData object."><meta property="og:description" content="
+This creates a Q-Q plot of the library sizes of the AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
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+
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Q-Q Plot of Library Sizes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>draw_libsize_qq.Rd</code></div>
     </div>
 
@@ -76,23 +51,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>color</dt>
+<dt id="arg-color">color<a class="anchor" aria-label="anchor" href="#arg-color"></a></dt>
 <dd><p>(<code>string</code>)<br> color of Q-Q line.</p></dd>
 
 
-<dt>linetype</dt>
+<dt id="arg-linetype">linetype<a class="anchor" aria-label="anchor" href="#arg-linetype"></a></dt>
 <dd><p>(<code>string</code>)<br> line type of  Q-Q line.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> object with the Q-Q Plot.</p>
+    <p>The <code>ggplot</code> object with the Q-Q Plot.</p>
     </div>
 
     <div class="section level2">
@@ -109,7 +84,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_libsize_qq-3.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -118,14 +93,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_nonzero_boxplot-1.png b/main/reference/draw_nonzero_boxplot-1.png
index f83de546..b876a71f 100644
Binary files a/main/reference/draw_nonzero_boxplot-1.png and b/main/reference/draw_nonzero_boxplot-1.png differ
diff --git a/main/reference/draw_nonzero_boxplot-2.png b/main/reference/draw_nonzero_boxplot-2.png
index 553495d0..f57ac9a2 100644
Binary files a/main/reference/draw_nonzero_boxplot-2.png and b/main/reference/draw_nonzero_boxplot-2.png differ
diff --git a/main/reference/draw_nonzero_boxplot.html b/main/reference/draw_nonzero_boxplot.html
index cdad444f..5be8d4fd 100644
--- a/main/reference/draw_nonzero_boxplot.html
+++ b/main/reference/draw_nonzero_boxplot.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Boxplot of Non-Zero Genes — draw_nonzero_boxplot • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Boxplot of Non-Zero Genes — draw_nonzero_boxplot"><meta name="description" content="
 This draws a boxplot, with overlaid data points, of the number of
-non-zero expressed genes per sample."><title>Boxplot of Non-Zero Genes — draw_nonzero_boxplot • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Boxplot of Non-Zero Genes — draw_nonzero_boxplot"><meta property="og:description" content="
+non-zero expressed genes per sample."><meta property="og:description" content="
 This draws a boxplot, with overlaid data points, of the number of
-non-zero expressed genes per sample."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Boxplot of Non-Zero Genes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>draw_nonzero_boxplot.Rd</code></div>
     </div>
 
@@ -79,23 +54,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>position</dt>
+<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
 <dd><p>(<code>Position</code>)<br> specifies x-axis position of points, e.g. for jittering.</p></dd>
 
 
-<dt>alpha</dt>
+<dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a></dt>
 <dd><p>(<code>proportion</code>)<br> specifies transparency of points.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> object with the boxplot.</p>
+    <p>The <code>ggplot</code> object with the boxplot.</p>
     </div>
 
     <div class="section level2">
@@ -113,7 +88,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_nonzero_boxplot-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -122,14 +97,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/draw_scatterplot-1.png b/main/reference/draw_scatterplot-1.png
index 60233ae1..2a4322c3 100644
Binary files a/main/reference/draw_scatterplot-1.png and b/main/reference/draw_scatterplot-1.png differ
diff --git a/main/reference/draw_scatterplot-2.png b/main/reference/draw_scatterplot-2.png
index 5e631676..0768c54a 100644
Binary files a/main/reference/draw_scatterplot-2.png and b/main/reference/draw_scatterplot-2.png differ
diff --git a/main/reference/draw_scatterplot.html b/main/reference/draw_scatterplot.html
index 712485f6..a18e3174 100644
--- a/main/reference/draw_scatterplot.html
+++ b/main/reference/draw_scatterplot.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This produces a scatterplot of two genes or gene signatures."><title>Scatterplot for Gene Expression Values — draw_scatterplot • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Scatterplot for Gene Expression Values — draw_scatterplot"><meta property="og:description" content="
-This produces a scatterplot of two genes or gene signatures."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Scatterplot for Gene Expression Values — draw_scatterplot • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Scatterplot for Gene Expression Values — draw_scatterplot"><meta name="description" content="
+This produces a scatterplot of two genes or gene signatures."><meta property="og:description" content="
+This produces a scatterplot of two genes or gene signatures."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Scatterplot for Gene Expression Values</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/draw_scatterplot.R" class="external-link"><code>R/draw_scatterplot.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/draw_scatterplot.R" class="external-link"><code>R/draw_scatterplot.R</code></a></small>
       <div class="d-none name"><code>draw_scatterplot.Rd</code></div>
     </div>
 
@@ -84,42 +59,42 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> selects assay from input.</p></dd>
 
 
-<dt>x_spec</dt>
+<dt id="arg-x-spec">x_spec<a class="anchor" aria-label="anchor" href="#arg-x-spec"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> gene specification for the x-axis.</p></dd>
 
 
-<dt>y_spec</dt>
+<dt id="arg-y-spec">y_spec<a class="anchor" aria-label="anchor" href="#arg-y-spec"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> gene specification for the y-axis.</p></dd>
 
 
-<dt>color_var</dt>
+<dt id="arg-color-var">color_var<a class="anchor" aria-label="anchor" href="#arg-color-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional color variable, taken
 from input sample variables.</p></dd>
 
 
-<dt>facet_var</dt>
+<dt id="arg-facet-var">facet_var<a class="anchor" aria-label="anchor" href="#arg-facet-var"></a></dt>
 <dd><p>(<code>string</code> or <code>NULL</code>)<br> optional faceting variable, taken
 from input sample variables.</p></dd>
 
 
-<dt>smooth_method</dt>
+<dt id="arg-smooth-method">smooth_method<a class="anchor" aria-label="anchor" href="#arg-smooth-method"></a></dt>
 <dd><p>(<code>string</code>)<br> smoothing method to use, either linear
 regression line (<code>lm</code>), local polynomial regression (<code>loess</code>) or <code>none</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>ggplot</code> scatterplot.</p>
+    <p>The <code>ggplot</code> scatterplot.</p>
     </div>
 
     <div class="section level2">
@@ -154,7 +129,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="draw_scatterplot-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -163,14 +138,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/expect_proportion.html b/main/reference/expect_proportion.html
new file mode 100644
index 00000000..fec621f4
--- /dev/null
+++ b/main/reference/expect_proportion.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/check_proportion.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/check_proportion.html">
+  </head>
+</html>
+
diff --git a/main/reference/expression_set.html b/main/reference/expression_set.html
index 067e8fd4..e12d2414 100644
--- a/main/reference/expression_set.html
+++ b/main/reference/expression_set.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Example ExpressionSet Data — expression_set • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example ExpressionSet Data — expression_set"><meta name="description" content="
 This example data can be used to try out conversion of a Biobase::ExpressionSet
-object into a HermesData object."><title>Example ExpressionSet Data — expression_set • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example ExpressionSet Data — expression_set"><meta property="og:description" content="
+object into a HermesData object."><meta property="og:description" content="
 This example data can be used to try out conversion of a Biobase::ExpressionSet
-object into a HermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+object into a HermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Example <code>ExpressionSet</code> Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>expression_set.Rd</code></div>
     </div>
 
@@ -90,13 +65,13 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
     <div class="dont-index">
 <ul><li><p><code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.html" class="external-link">SummarizedExperiment::makeSummarizedExperimentFromExpressionSet()</a></code> to convert into a
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p></li>
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p></li>
 <li><p><code><a href="summarized_experiment.html">summarized_experiment</a></code> which contains similar data already as a
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p></li>
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p></li>
 </ul></div>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -105,14 +80,14 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/extraColDataNames,AnyHermesData-method.html b/main/reference/extraColDataNames,AnyHermesData-method.html
new file mode 100644
index 00000000..3124a7f5
--- /dev/null
+++ b/main/reference/extraColDataNames,AnyHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/extra_data_names.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/extra_data_names.html">
+  </head>
+</html>
+
diff --git a/main/reference/extraColDataNames.html b/main/reference/extraColDataNames.html
new file mode 100644
index 00000000..3124a7f5
--- /dev/null
+++ b/main/reference/extraColDataNames.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/extra_data_names.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/extra_data_names.html">
+  </head>
+</html>
+
diff --git a/main/reference/extraRowDataNames,AnyHermesData-method.html b/main/reference/extraRowDataNames,AnyHermesData-method.html
new file mode 100644
index 00000000..3124a7f5
--- /dev/null
+++ b/main/reference/extraRowDataNames,AnyHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/extra_data_names.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/extra_data_names.html">
+  </head>
+</html>
+
diff --git a/main/reference/extraRowDataNames.html b/main/reference/extraRowDataNames.html
new file mode 100644
index 00000000..3124a7f5
--- /dev/null
+++ b/main/reference/extraRowDataNames.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/extra_data_names.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/extra_data_names.html">
+  </head>
+</html>
+
diff --git a/main/reference/extra_data_names.html b/main/reference/extra_data_names.html
index c3cd4fb4..8f5467c3 100644
--- a/main/reference/extra_data_names.html
+++ b/main/reference/extra_data_names.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Extra Variable Names Accessor Methods — extra_data_names • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extra Variable Names Accessor Methods — extra_data_names"><meta name="description" content="
 The methods access the names of the variables in colData() and rowData() of
 the object which are not required by design. So these can be additional sample or
-patient characteristics, or gene characteristics."><title>Extra Variable Names Accessor Methods — extra_data_names • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extra Variable Names Accessor Methods — extra_data_names"><meta property="og:description" content="
+patient characteristics, or gene characteristics."><meta property="og:description" content="
 The methods access the names of the variables in colData() and rowData() of
 the object which are not required by design. So these can be additional sample or
-patient characteristics, or gene characteristics."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+patient characteristics, or gene characteristics."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Extra Variable Names Accessor Methods</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>extra_data_names.Rd</code></div>
     </div>
 
@@ -79,30 +54,30 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extraColDataNames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">extraColDataNames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">extraRowDataNames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">extraRowDataNames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>not used.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The character vector with the additional variable names in either
+    <p>The character vector with the additional variable names in either
 <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData()</a></code> or <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData()</a></code>.</p>
     </div>
 
@@ -126,7 +101,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "GeneID"          "SYMBOL"          "chromosome_name"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -135,14 +110,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/filter,AnyHermesData-method.html b/main/reference/filter,AnyHermesData-method.html
new file mode 100644
index 00000000..51759f8a
--- /dev/null
+++ b/main/reference/filter,AnyHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/filter.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/filter.html">
+  </head>
+</html>
+
diff --git a/main/reference/filter,data.frame-method.html b/main/reference/filter,data.frame-method.html
new file mode 100644
index 00000000..51759f8a
--- /dev/null
+++ b/main/reference/filter,data.frame-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/filter.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/filter.html">
+  </head>
+</html>
+
diff --git a/main/reference/filter,ts-method.html b/main/reference/filter,ts-method.html
new file mode 100644
index 00000000..51759f8a
--- /dev/null
+++ b/main/reference/filter,ts-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/filter.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/filter.html">
+  </head>
+</html>
+
diff --git a/main/reference/filter.html b/main/reference/filter.html
index 0e5975cf..1d9a3f4b 100644
--- a/main/reference/filter.html
+++ b/main/reference/filter.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This filters a AnyHermesData object using the default QC flags and required annotations."><title>Filter AnyHermesData on Subset Passing Default QC Flags — filter • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Filter AnyHermesData on Subset Passing Default QC Flags — filter"><meta property="og:description" content="
-This filters a AnyHermesData object using the default QC flags and required annotations."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Filter AnyHermesData on Subset Passing Default QC Flags — filter • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Filter AnyHermesData on Subset Passing Default QC Flags — filter"><meta name="description" content="
+This filters a AnyHermesData object using the default QC flags and required annotations."><meta property="og:description" content="
+This filters a AnyHermesData object using the default QC flags and required annotations."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Filter <code>AnyHermesData</code> on Subset Passing Default QC Flags</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/dplyr_compatibility.R" class="external-link"><code>R/dplyr_compatibility.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/main/R/dplyr_compatibility.R" class="external-link"><code>R/dplyr_compatibility.R</code></a></small>
       <div class="d-none name"><code>filter.Rd</code></div>
     </div>
 
@@ -73,44 +48,44 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">filter</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">filter</span><span class="op">(</span><span class="va">object</span>, what <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"genes"</span>, <span class="st">"samples"</span><span class="op">)</span>, annotation_required <span class="op">=</span> <span class="st">"size"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for data.frame</span></span>
+<span><span class="co"># S4 method for class 'data.frame'</span></span>
 <span><span class="fu">filter</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for ts</span></span>
+<span><span class="co"># S4 method for class 'ts'</span></span>
 <span><span class="fu">filter</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to filter.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments.</p></dd>
 
 
-<dt>what</dt>
+<dt id="arg-what">what<a class="anchor" aria-label="anchor" href="#arg-what"></a></dt>
 <dd><p>(<code>character</code>)<br> specify whether to apply the filter on <code>genes</code> and / or <code>samples</code>.</p></dd>
 
 
-<dt>annotation_required</dt>
+<dt id="arg-annotation-required">annotation_required<a class="anchor" aria-label="anchor" href="#arg-annotation-required"></a></dt>
 <dd><p>(<code>character</code>)<br> names of required <code><a href="annotation.html">annotation</a></code> columns for genes. Only
 used when <code>genes</code> are filtered.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The filtered <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
+    <p>The filtered <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>Only genes without low expression (<code>low_expression_flag</code>) and samples
 without low depth (<code>low_depth_flag</code>) or technical failure (<code>tech_failure_flag</code>)
 remain in the returned filtered object.</p></li>
@@ -145,7 +120,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">filter</span><span class="op">(</span><span class="va">a</span>, what <span class="op">=</span> <span class="st">"genes"</span>, annotation_required <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"size"</span><span class="op">)</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -154,14 +129,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/gene_spec.html b/main/reference/gene_spec.html
index 58a73d1d..582de515 100644
--- a/main/reference/gene_spec.html
+++ b/main/reference/gene_spec.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-Creates a new GeneSpec object."><title>GeneSpec Constructor — gene_spec • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GeneSpec Constructor — gene_spec"><meta property="og:description" content="
-Creates a new GeneSpec object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GeneSpec Constructor — gene_spec • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="GeneSpec Constructor — gene_spec"><meta name="description" content="
+Creates a new GeneSpec object."><meta property="og:description" content="
+Creates a new GeneSpec object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>GeneSpec</code> Constructor</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
       <div class="d-none name"><code>gene_spec.Rd</code></div>
     </div>
 
@@ -76,26 +51,26 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>genes</dt>
+
+
+<dl><dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(named <code>character</code> or <code>NULL</code>)<br> the gene IDs, where the names
 are used as labels if available.</p></dd>
 
 
-<dt>fun</dt>
+<dt id="arg-fun">fun<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
 <dd><p>(<code>function</code> or <code>NULL</code>)<br> summary function. If <code>NULL</code> is
 used then multiple genes are not summarized but returned as a matrix from the
 <code>extract</code> method.</p></dd>
 
 
-<dt>fun_name</dt>
+<dt id="arg-fun-name">fun_name<a class="anchor" aria-label="anchor" href="#arg-fun-name"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the summary function.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A new <code><a href="GeneSpec.html">GeneSpec</a></code> object.</p>
+    <p>A new <code><a href="GeneSpec.html">GeneSpec</a></code> object.</p>
     </div>
 
     <div class="section level2">
@@ -134,7 +109,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>     genes: GeneID:11185 GeneID:10677 GeneID:101928428</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -143,14 +118,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/genes,AnyHermesData-method.html b/main/reference/genes,AnyHermesData-method.html
new file mode 100644
index 00000000..b8003ffb
--- /dev/null
+++ b/main/reference/genes,AnyHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/genes.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/genes.html">
+  </head>
+</html>
+
diff --git a/main/reference/genes.html b/main/reference/genes.html
index 5441e3b3..e9f70e5f 100644
--- a/main/reference/genes.html
+++ b/main/reference/genes.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Gene IDs Accessor — genes • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Gene IDs Accessor — genes"><meta name="description" content="
 Access the gene IDs, i.e. row names, of a AnyHermesData object with a
-nicely named accessor method."><title>Gene IDs Accessor — genes • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Gene IDs Accessor — genes"><meta property="og:description" content="
+nicely named accessor method."><meta property="og:description" content="
 Access the gene IDs, i.e. row names, of a AnyHermesData object with a
-nicely named accessor method."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Gene IDs Accessor</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>genes.Rd</code></div>
     </div>
 
@@ -76,21 +51,21 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">genes</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">genes</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The character vector with the gene IDs.</p>
+    <p>The character vector with the gene IDs.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -1798,7 +1773,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [5083] "GeneID:9084"      "GeneID:9087"      "GeneID:9426"     </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -1807,14 +1782,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/get_low_depth.html b/main/reference/get_low_depth.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/get_low_depth.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/get_low_expression.html b/main/reference/get_low_expression.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/get_low_expression.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/get_tech_failure.html b/main/reference/get_tech_failure.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/get_tech_failure.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_all_duplicated.html b/main/reference/h_all_duplicated.html
index de3c8434..4454ee75 100644
--- a/main/reference/h_all_duplicated.html
+++ b/main/reference/h_all_duplicated.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The difference here to duplicated() is that also the first occurrence
-of a duplicate is flagged as TRUE."><title>Finding All Duplicates in Vector — h_all_duplicated • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Finding All Duplicates in Vector — h_all_duplicated"><meta property="og:description" content="The difference here to duplicated() is that also the first occurrence
-of a duplicate is flagged as TRUE."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Finding All Duplicates in Vector — h_all_duplicated • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Finding All Duplicates in Vector — h_all_duplicated"><meta name="description" content="The difference here to duplicated() is that also the first occurrence
+of a duplicate is flagged as TRUE."><meta property="og:description" content="The difference here to duplicated() is that also the first occurrence
+of a duplicate is flagged as TRUE."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Finding All Duplicates in Vector</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>h_all_duplicated.Rd</code></div>
     </div>
 
@@ -76,15 +51,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>a vector or a data frame or an array or <code>NULL</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Logical vector flagging all occurrences of duplicate values as <code>TRUE</code>.</p>
+    <p>Logical vector flagging all occurrences of duplicate values as <code>TRUE</code>.</p>
     </div>
 
     <div class="section level2">
@@ -95,7 +70,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE  TRUE FALSE</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -104,14 +79,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_cpm.html b/main/reference/h_cpm.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_cpm.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/normalize.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_df_factors_with_explicit_na.html b/main/reference/h_df_factors_with_explicit_na.html
index d6815555..855f4c9e 100644
--- a/main/reference/h_df_factors_with_explicit_na.html
+++ b/main/reference/h_df_factors_with_explicit_na.html
@@ -1,16 +1,13 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
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 This helper function converts all character and logical variables
 to factor variables in a data.frame. It also sets an explicit missing data level
 for all factor variables that have at least one NA. Empty strings are handled
-as NA."><title>Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na"><meta property="og:description" content="
+as NA."><meta property="og:description" content="
 This helper function converts all character and logical variables
 to factor variables in a data.frame. It also sets an explicit missing data level
 for all factor variables that have at least one NA. Empty strings are handled
-as NA."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+as NA."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -18,55 +15,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Conversion to Factors with Explicit Missing Level in a <code>data.frame</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>h_df_factors_with_explicit_na.Rd</code></div>
     </div>
 
@@ -85,19 +60,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>data</dt>
+
+
+<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
 <dd><p>(<code>data.frame</code>)<br> input data with at least one column.</p></dd>
 
 
-<dt>na_level</dt>
+<dt id="arg-na-level">na_level<a class="anchor" aria-label="anchor" href="#arg-na-level"></a></dt>
 <dd><p>(<code>string</code>)<br> explicit missing level to be used.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The modified data.</p>
+    <p>The modified data.</p>
     </div>
 
     <div class="section level2">
@@ -115,7 +90,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2  2 &lt;Missing&gt; D         X Z</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -124,14 +99,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_diff_expr_deseq2.html b/main/reference/h_diff_expr_deseq2.html
index 33244e81..f34511e2 100644
--- a/main/reference/h_diff_expr_deseq2.html
+++ b/main/reference/h_diff_expr_deseq2.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>DESeq2 Differential Expression Analysis — h_diff_expr_deseq2 • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DESeq2 Differential Expression Analysis — h_diff_expr_deseq2"><meta name="description" content="
 This helper functions performs the differential expression analysis with
-DESeq2::DESeq() for a given AnyHermesData input and design matrix."><title>DESeq2 Differential Expression Analysis — h_diff_expr_deseq2 • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DESeq2 Differential Expression Analysis — h_diff_expr_deseq2"><meta property="og:description" content="
+DESeq2::DESeq() for a given AnyHermesData input and design matrix."><meta property="og:description" content="
 This helper functions performs the differential expression analysis with
-DESeq2::DESeq() for a given AnyHermesData input and design matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+DESeq2::DESeq() for a given AnyHermesData input and design matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>DESeq2</code> Differential Expression Analysis</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
       <div class="d-none name"><code>h_diff_expr_deseq2.Rd</code></div>
     </div>
 
@@ -79,33 +54,29 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>HermesData</code>)<br> input.</p></dd>
 
 
-<dt>design</dt>
+<dt id="arg-design">design<a class="anchor" aria-label="anchor" href="#arg-design"></a></dt>
 <dd><p>(<code>matrix</code>)<br> design matrix.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments internally passed to <code><a href="https://rdrr.io/pkg/DESeq2/man/DESeq.html" class="external-link">DESeq2::DESeq()</a></code> (<code>fitType</code>, <code>sfType</code>,
 <code>minReplicatesForReplace</code>, <code>useT</code>, <code>minmu</code>).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame with columns <code>log2_fc</code> (estimated log2 fold change),
+    <p>A data frame with columns <code>log2_fc</code> (estimated log2 fold change),
 <code>stat</code> (Wald statistic), <code>p_val</code> (raw p-value), <code>adj_p_pval</code> (Benjamini-Hochberg adjusted p-value).</p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Love MI, Huber W, Anders S (2014).
-“Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.”
-<em>Genome Biology</em>, <b>15</b>(12), 550.
-<a href="https://doi.org/10.1186/s13059-014-0550-8" class="external-link">doi:10.1186/s13059-014-0550-8</a>
-.</p>
+    <p>DESeq2_packagehermes</p>
     </div>
 
     <div class="section level2">
@@ -138,7 +109,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> GeneID:51575  -0.7889652 -4.255997 2.081193e-05 0.0076822022</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -147,14 +118,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_diff_expr_voom.html b/main/reference/h_diff_expr_voom.html
index 3d81c628..8c472b91 100644
--- a/main/reference/h_diff_expr_voom.html
+++ b/main/reference/h_diff_expr_voom.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>limma/voom Differential Expression Analysis — h_diff_expr_voom • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="limma/voom Differential Expression Analysis — h_diff_expr_voom"><meta name="description" content="
 This helper functions performs the differential expression analysis with the voom
 method from the limma package (via limma::voom(), limma::lmFit() and limma::eBayes())
-for given counts in a AnyHermesData object and a corresponding design matrix."><title>limma/voom Differential Expression Analysis — h_diff_expr_voom • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="limma/voom Differential Expression Analysis — h_diff_expr_voom"><meta property="og:description" content="
+for given counts in a AnyHermesData object and a corresponding design matrix."><meta property="og:description" content="
 This helper functions performs the differential expression analysis with the voom
 method from the limma package (via limma::voom(), limma::lmFit() and limma::eBayes())
-for given counts in a AnyHermesData object and a corresponding design matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+for given counts in a AnyHermesData object and a corresponding design matrix."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>limma</code>/voom Differential Expression Analysis</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/differential.R" class="external-link"><code>R/differential.R</code></a></small>
       <div class="d-none name"><code>h_diff_expr_voom.Rd</code></div>
     </div>
 
@@ -82,38 +57,30 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>design</dt>
+<dt id="arg-design">design<a class="anchor" aria-label="anchor" href="#arg-design"></a></dt>
 <dd><p>(<code>matrix</code>)<br> design matrix.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments internally passed to <code><a href="https://rdrr.io/pkg/limma/man/ebayes.html" class="external-link">limma::eBayes()</a></code> (<code>robust</code>, <code>trend</code>, <code>proportion</code>,
 <code>winsor.tail.p</code>, <code>stdev.coef.lim</code>).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame with columns <code>log2_fc</code> (estimated log2 fold change),
+    <p>A data frame with columns <code>log2_fc</code> (estimated log2 fold change),
 <code>stat</code> (moderated t-statistic), <code>p_val</code> (raw p-value), <code>adj_p_pval</code> (Benjamini-Hochberg adjusted p-value).</p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015).
-“limma powers differential expression analyses for RNA-sequencing and microarray studies.”
-<em>Nucleic Acids Research</em>, <b>43</b>(7), e47.
-<a href="https://doi.org/10.1093/nar/gkv007" class="external-link">doi:10.1093/nar/gkv007</a>
-.</p>
-<p>Law CW, Chen Y, Shi W, Smyth GK (2014).
-“voom: precision weights unlock linear model analysis tools for RNA-seq read counts.”
-<em>Genome Biology</em>, <b>15</b>(2), R29.
-<a href="https://doi.org/10.1186/gb-2014-15-2-r29" class="external-link">doi:10.1186/gb-2014-15-2-r29</a>
-.</p>
+    <p>limma_packagehermes</p>
+<p>voom_methodhermes</p>
     </div>
 
     <div class="section level2">
@@ -146,7 +113,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> GeneID:123036  2.9002547  3.431263 0.0024329189 0.8995289</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -155,14 +122,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_draw_boxplot_df.html b/main/reference/h_draw_boxplot_df.html
new file mode 100644
index 00000000..7dbbbf12
--- /dev/null
+++ b/main/reference/h_draw_boxplot_df.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/draw_boxplot.html" />
+    <meta name="robots" content="noindex">
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+
diff --git a/main/reference/h_ensembl_to_entrez_ids.html b/main/reference/h_ensembl_to_entrez_ids.html
index 77379017..0f8f44e8 100644
--- a/main/reference/h_ensembl_to_entrez_ids.html
+++ b/main/reference/h_ensembl_to_entrez_ids.html
@@ -1,10 +1,7 @@
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-This helper function queries BioMart to translate Ensembl to Entrez Gene IDs."><title>Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids"><meta property="og:description" content="
-This helper function queries BioMart to translate Ensembl to Entrez Gene IDs."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids"><meta name="description" content="
+This helper function queries BioMart to translate Ensembl to Entrez Gene IDs."><meta property="og:description" content="
+This helper function queries BioMart to translate Ensembl to Entrez Gene IDs."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-<!-- end dropdown for versions -->
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Translation of <code>Ensembl</code> to <code>Entrez</code> Gene IDs</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>h_ensembl_to_entrez_ids.Rd</code></div>
     </div>
 
@@ -76,19 +51,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gene_ids</dt>
+
+
+<dl><dt id="arg-gene-ids">gene_ids<a class="anchor" aria-label="anchor" href="#arg-gene-ids"></a></dt>
 <dd><p>(<code>character</code>)<br><code>Ensembl</code> gene IDs.</p></dd>
 
 
-<dt>mart</dt>
+<dt id="arg-mart">mart<a class="anchor" aria-label="anchor" href="#arg-mart"></a></dt>
 <dd><p>(<code>Mart</code>)<br> given <code><a href="https://rdrr.io/pkg/biomaRt/man/Mart-class.html" class="external-link">biomaRt::Mart</a></code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Character vector of <code>Entrez</code> gene IDs.</p>
+    <p>Character vector of <code>Entrez</code> gene IDs.</p>
     </div>
 
     <div class="section level2">
@@ -99,7 +74,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -108,14 +83,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_get_annotation_biomart.html b/main/reference/h_get_annotation_biomart.html
index 08b98501..80aaaef8 100644
--- a/main/reference/h_get_annotation_biomart.html
+++ b/main/reference/h_get_annotation_biomart.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get Annotations from BioMart — h_get_annotation_biomart • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Annotations from BioMart — h_get_annotation_biomart"><meta name="description" content="
 Helper function to query annotations from biomaRt, for cleaned up gene IDs of
-a specific ID variable and given biomaRt::Mart."><title>Get Annotations from BioMart — h_get_annotation_biomart • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get Annotations from BioMart — h_get_annotation_biomart"><meta property="og:description" content="
+a specific ID variable and given biomaRt::Mart."><meta property="og:description" content="
 Helper function to query annotations from biomaRt, for cleaned up gene IDs of
-a specific ID variable and given biomaRt::Mart."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+a specific ID variable and given biomaRt::Mart."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Get Annotations from <code>BioMart</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>h_get_annotation_biomart.Rd</code></div>
     </div>
 
@@ -79,25 +54,25 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gene_ids</dt>
+
+
+<dl><dt id="arg-gene-ids">gene_ids<a class="anchor" aria-label="anchor" href="#arg-gene-ids"></a></dt>
 <dd><p>(<code>character</code>)<br> gene IDs, e.g. <code>10329</code>, i.e. already
 without the <code>Entrez</code> <code>GeneID</code> prefix, or <code>ENSG00000241644</code> for <code>Ensembl</code> gene ID.</p></dd>
 
 
-<dt>id_var</dt>
+<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a></dt>
 <dd><p>(<code>string</code>)<br> corresponding gene ID variable name in <code>BioMart</code>,
 i.e. <code>entrezgene_id</code> or <code>ensembl_gene_id</code>.</p></dd>
 
 
-<dt>mart</dt>
+<dt id="arg-mart">mart<a class="anchor" aria-label="anchor" href="#arg-mart"></a></dt>
 <dd><p>(<code>Mart</code>)<br> given <code><a href="https://rdrr.io/pkg/biomaRt/man/Mart-class.html" class="external-link">biomaRt::Mart</a></code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame with columns:</p><ul><li><p><code>id_var</code> (depending on what was used)</p></li>
+    <p>A data frame with columns:</p><ul><li><p><code>id_var</code> (depending on what was used)</p></li>
 <li><p><code>hgnc_symbol</code></p></li>
 <li><p><code>entrezgene_description</code></p></li>
 <li><p><code>chromosome_name</code></p></li>
@@ -114,7 +89,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -123,14 +98,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_get_granges_by_id.html b/main/reference/h_get_granges_by_id.html
index 9da1d4e9..ede54e8e 100644
--- a/main/reference/h_get_granges_by_id.html
+++ b/main/reference/h_get_granges_by_id.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id"><meta name="description" content="
 This function extracts the chromosome number, the start position and the end position of transcripts
 in given data.frame with coordinates as returned by biomaRt::getBM() and converts
-them to a GRanges object."><title>Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id"><meta property="og:description" content="
+them to a GRanges object."><meta property="og:description" content="
 This function extracts the chromosome number, the start position and the end position of transcripts
 in given data.frame with coordinates as returned by biomaRt::getBM() and converts
-them to a GRanges object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+them to a GRanges object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-</li>
-<li class="active nav-item">
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-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Conversion of <code>BioMart</code> Coordinates into <code>GRanges</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>h_get_granges_by_id.Rd</code></div>
     </div>
 
@@ -82,20 +57,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>coords</dt>
+
+
+<dl><dt id="arg-coords">coords<a class="anchor" aria-label="anchor" href="#arg-coords"></a></dt>
 <dd><p>(<code>data.frame</code>)<br> as returned by <code><a href="https://rdrr.io/pkg/biomaRt/man/getBM.html" class="external-link">biomaRt::getBM()</a></code>, containing the columns
 <code>ensembl_gene_id</code>, <code>chromosome_name</code>, <code>exon_chrom_start</code>, <code>exon_chrom_end</code>.</p></dd>
 
 
-<dt>id</dt>
+<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
 <dd><p>(<code>string</code>)<br> single <code>Ensembl</code> gene ID to convert the coordinates for.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>GRange</code> objects for the respective single gene ID.</p>
+    <p><code>GRange</code> objects for the respective single gene ID.</p>
     </div>
 
     <div class="section level2">
@@ -119,7 +94,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -128,14 +103,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_get_size_biomart.html b/main/reference/h_get_size_biomart.html
index fb84dc69..5caf735b 100644
--- a/main/reference/h_get_size_biomart.html
+++ b/main/reference/h_get_size_biomart.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Total Length of All Exons for Genes — h_get_size_biomart • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total Length of All Exons for Genes — h_get_size_biomart"><meta name="description" content="
 This helper function queries BioMart for lengths of genes by adding up all
-exon lengths after reducing overlaps."><title>Total Length of All Exons for Genes — h_get_size_biomart • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total Length of All Exons for Genes — h_get_size_biomart"><meta property="og:description" content="
+exon lengths after reducing overlaps."><meta property="og:description" content="
 This helper function queries BioMart for lengths of genes by adding up all
-exon lengths after reducing overlaps."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+exon lengths after reducing overlaps."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Total Length of All Exons for Genes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>h_get_size_biomart.Rd</code></div>
     </div>
 
@@ -79,25 +54,25 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gene_ids</dt>
+
+
+<dl><dt id="arg-gene-ids">gene_ids<a class="anchor" aria-label="anchor" href="#arg-gene-ids"></a></dt>
 <dd><p>(<code>character</code>)<br> gene IDs, e.g. <code>10329</code>, i.e. already
 without the <code>Entrez</code> <code>GeneID</code> prefix, or <code>ENSG00000241644</code> for <code>Ensembl</code> gene ID.</p></dd>
 
 
-<dt>id_var</dt>
+<dt id="arg-id-var">id_var<a class="anchor" aria-label="anchor" href="#arg-id-var"></a></dt>
 <dd><p>(<code>string</code>)<br> corresponding gene ID variable name in <code>BioMart</code>,
 i.e. <code>entrezgene_id</code> or <code>ensembl_gene_id</code>.</p></dd>
 
 
-<dt>mart</dt>
+<dt id="arg-mart">mart<a class="anchor" aria-label="anchor" href="#arg-mart"></a></dt>
 <dd><p>(<code>Mart</code>)<br> given <code><a href="https://rdrr.io/pkg/biomaRt/man/Mart-class.html" class="external-link">biomaRt::Mart</a></code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Named integer vector indicating the gene lengths.</p>
+    <p>Named integer vector indicating the gene lengths.</p>
     </div>
 
     <div class="section level2">
@@ -111,7 +86,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -120,14 +95,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_has_req_annotations.html b/main/reference/h_has_req_annotations.html
index 72ccd477..6db44ed9 100644
--- a/main/reference/h_has_req_annotations.html
+++ b/main/reference/h_has_req_annotations.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Predicate for Required Annotations — h_has_req_annotations • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Predicate for Required Annotations — h_has_req_annotations"><meta name="description" content="
 This helper function determines for each gene in the object whether all required
-annotation columns are filled."><title>Predicate for Required Annotations — h_has_req_annotations • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Predicate for Required Annotations — h_has_req_annotations"><meta property="og:description" content="
+annotation columns are filled."><meta property="og:description" content="
 This helper function determines for each gene in the object whether all required
-annotation columns are filled."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -14,55 +11,33 @@
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
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+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Predicate for Required Annotations</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>h_has_req_annotations.Rd</code></div>
     </div>
 
@@ -79,19 +54,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input object.</p></dd>
 
 
-<dt>annotation_required</dt>
+<dt id="arg-annotation-required">annotation_required<a class="anchor" aria-label="anchor" href="#arg-annotation-required"></a></dt>
 <dd><p>(<code>character</code>)<br> names of required <code><a href="annotation.html">annotation</a></code> columns for genes.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Named logical vector with one value for each gene in <code>object</code>, which is <code>TRUE</code> if all
+    <p>Named logical vector with one value for each gene in <code>object</code>, which is <code>TRUE</code> if all
 required annotation columns are filled, and otherwise <code>FALSE</code>.</p>
     </div>
     <div class="section level2">
@@ -111,7 +86,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>            1 </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -120,14 +95,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_low_depth_flag.html b/main/reference/h_low_depth_flag.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/h_low_depth_flag.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_low_expression_flag.html b/main/reference/h_low_expression_flag.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/h_low_expression_flag.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_map_pos.html b/main/reference/h_map_pos.html
index 2575075e..8e2fd1e7 100644
--- a/main/reference/h_map_pos.html
+++ b/main/reference/h_map_pos.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This is used by the rename method. It wraps the assertions and the
-matching used several times."><title>Helper Function For Matching Map Values to Names — h_map_pos • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper Function For Matching Map Values to Names — h_map_pos"><meta property="og:description" content="This is used by the rename method. It wraps the assertions and the
-matching used several times."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Helper Function For Matching Map Values to Names — h_map_pos • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper Function For Matching Map Values to Names — h_map_pos"><meta name="description" content="This is used by the rename method. It wraps the assertions and the
+matching used several times."><meta property="og:description" content="This is used by the rename method. It wraps the assertions and the
+matching used several times."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
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-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Helper Function For Matching Map Values to Names</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>h_map_pos.Rd</code></div>
     </div>
 
@@ -76,20 +51,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>names</dt>
+
+
+<dl><dt id="arg-names">names<a class="anchor" aria-label="anchor" href="#arg-names"></a></dt>
 <dd><p>(<code>character</code>)<br> original names.</p></dd>
 
 
-<dt>map</dt>
+<dt id="arg-map">map<a class="anchor" aria-label="anchor" href="#arg-map"></a></dt>
 <dd><p>(named <code>character</code>)<br> the mapping vector from old (value) to new
 (name) names. All values must be included in <code>names</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Integer vector of the positions of the <code>map</code> values in the <code>names</code>.</p>
+    <p>Integer vector of the positions of the <code>map</code> values in the <code>names</code>.</p>
     </div>
 
     <div class="section level2">
@@ -98,7 +73,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -107,14 +82,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_parens.html b/main/reference/h_parens.html
index 9eda44bd..ee0e0e74 100644
--- a/main/reference/h_parens.html
+++ b/main/reference/h_parens.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Parenthesize a Character Vector — h_parens • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parenthesize a Character Vector — h_parens"><meta name="description" content="
 This helper function adds parentheses around each element of a character
-vector."><title>Parenthesize a Character Vector — h_parens • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Parenthesize a Character Vector — h_parens"><meta property="og:description" content="
+vector."><meta property="og:description" content="
 This helper function adds parentheses around each element of a character
-vector."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+vector."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Parenthesize a Character Vector</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>h_parens.Rd</code></div>
     </div>
 
@@ -79,15 +54,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>character</code>)<br> inputs which should be parenthesized.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Character vector with parentheses, except when <code>x</code> is a blank string
+    <p>Character vector with parentheses, except when <code>x</code> is a blank string
 in which case it is returned unaltered.</p>
     </div>
 
@@ -101,7 +76,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "(bla)" "(bli)"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -110,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_pca_df_r2_matrix.html b/main/reference/h_pca_df_r2_matrix.html
index 9f0f2076..1d8b12e3 100644
--- a/main/reference/h_pca_df_r2_matrix.html
+++ b/main/reference/h_pca_df_r2_matrix.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix"><meta name="description" content="
 This function processes sample variables from AnyHermesData and the
-corresponding principal components matrix, and then generates the matrix of R2 values."><title>Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix"><meta property="og:description" content="
+corresponding principal components matrix, and then generates the matrix of R2 values."><meta property="og:description" content="
 This function processes sample variables from AnyHermesData and the
-corresponding principal components matrix, and then generates the matrix of R2 values."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+corresponding principal components matrix, and then generates the matrix of R2 values."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Calculation of R2 Matrix between Sample Variables and Principal Components</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
       <div class="d-none name"><code>h_pca_df_r2_matrix.Rd</code></div>
     </div>
 
@@ -79,25 +54,25 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>pca</dt>
+
+
+<dl><dt id="arg-pca">pca<a class="anchor" aria-label="anchor" href="#arg-pca"></a></dt>
 <dd><p>(<code>matrix</code>)<br> comprises principal components generated by <code><a href="calc_pca.html">calc_pca()</a></code>.</p></dd>
 
 
-<dt>df</dt>
+<dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
 <dd><p>(<code>data.frame</code>)<br> from the <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::colData()</a></code> of a
 <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A matrix with R2 values for all combinations of sample variables and principal
+    <p>A matrix with R2 values for all combinations of sample variables and principal
 components.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>Note that only the <code>df</code> columns which are <code>numeric</code>, <code>character</code>, <code>factor</code> or
 <code>logical</code> are included in the resulting matrix, because other variable types are not
 supported.</p></li>
@@ -139,7 +114,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 74</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -148,14 +123,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_pca_var_rsquared.html b/main/reference/h_pca_var_rsquared.html
index 91a58f05..28187eca 100644
--- a/main/reference/h_pca_var_rsquared.html
+++ b/main/reference/h_pca_var_rsquared.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared"><meta name="description" content="
 This helper function calculates R2 values between one sample variable from AnyHermesData
-and all Principal Components (PCs) separately (one linear model is fit for each PC)."><title>Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared"><meta property="og:description" content="
+and all Principal Components (PCs) separately (one linear model is fit for each PC)."><meta property="og:description" content="
 This helper function calculates R2 values between one sample variable from AnyHermesData
-and all Principal Components (PCs) separately (one linear model is fit for each PC)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+and all Principal Components (PCs) separately (one linear model is fit for each PC)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
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-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
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-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Calculation of R2 between Sample Variable and Principal Components</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
       <div class="d-none name"><code>h_pca_var_rsquared.Rd</code></div>
     </div>
 
@@ -79,19 +54,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>pca</dt>
+
+
+<dl><dt id="arg-pca">pca<a class="anchor" aria-label="anchor" href="#arg-pca"></a></dt>
 <dd><p>(<code>matrix</code>)<br> principal components matrix generated by <code><a href="calc_pca.html">calc_pca()</a></code>.</p></dd>
 
 
-<dt>x</dt>
+<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>vector</code>)<br> values of one sample variable from a <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A vector with R2 values for each principal component.</p>
+    <p>A vector with R2 values for each principal component.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -116,7 +91,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">r2</span> <span class="op">&lt;-</span> <span class="fu">h_pca_var_rsquared</span><span class="op">(</span><span class="va">pca</span>, <span class="va">x</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -125,14 +100,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/main/reference/h_rlog.html b/main/reference/h_rlog.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_rlog.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/normalize.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_rpkm.html b/main/reference/h_rpkm.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_rpkm.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
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+</html>
+
diff --git a/main/reference/h_short_list.html b/main/reference/h_short_list.html
index 0042be5c..190ec559 100644
--- a/main/reference/h_short_list.html
+++ b/main/reference/h_short_list.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Make a Short List of a Character Vector — h_short_list • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make a Short List of a Character Vector — h_short_list"><meta name="description" content='
 This helper function makes a short list string, e.g. "a, b, ..., z"
-out of a character vector, e.g. letters.'><title>Make a Short List of a Character Vector — h_short_list • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make a Short List of a Character Vector — h_short_list"><meta property="og:description" content='
+out of a character vector, e.g. letters.'><meta property="og:description" content='
 This helper function makes a short list string, e.g. "a, b, ..., z"
-out of a character vector, e.g. letters.'><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+out of a character vector, e.g. letters.'><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Make a Short List of a Character Vector</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>h_short_list.Rd</code></div>
     </div>
 
@@ -79,24 +54,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>character</code>)<br> input which should be listed.</p></dd>
 
 
-<dt>sep</dt>
+<dt id="arg-sep">sep<a class="anchor" aria-label="anchor" href="#arg-sep"></a></dt>
 <dd><p>(<code>string</code>)<br> separator to use.</p></dd>
 
 
-<dt>thresh</dt>
+<dt id="arg-thresh">thresh<a class="anchor" aria-label="anchor" href="#arg-thresh"></a></dt>
 <dd><p>(<code>count</code>)<br> threshold to use, if the length of <code>x</code> is larger
 then the list will be shortened using the <code>...</code> ellipsis.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>String with the short list.</p>
+    <p>String with the short list.</p>
     </div>
 
     <div class="section level2">
@@ -109,7 +84,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "A;B;C;D;E"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -118,14 +93,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_strip_prefix.html b/main/reference/h_strip_prefix.html
index ae71534e..54ea09b9 100644
--- a/main/reference/h_strip_prefix.html
+++ b/main/reference/h_strip_prefix.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Stripping Prefix from Gene IDs — h_strip_prefix • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stripping Prefix from Gene IDs — h_strip_prefix"><meta name="description" content="
 This helper function removes the prefix and possible delimiter from
-a vector of gene IDs, such that only the digits are returned."><title>Stripping Prefix from Gene IDs — h_strip_prefix • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Stripping Prefix from Gene IDs — h_strip_prefix"><meta property="og:description" content="
+a vector of gene IDs, such that only the digits are returned."><meta property="og:description" content="
 This helper function removes the prefix and possible delimiter from
-a vector of gene IDs, such that only the digits are returned."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+a vector of gene IDs, such that only the digits are returned."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Stripping Prefix from Gene IDs</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>h_strip_prefix.Rd</code></div>
     </div>
 
@@ -79,20 +54,20 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gene_ids</dt>
+
+
+<dl><dt id="arg-gene-ids">gene_ids<a class="anchor" aria-label="anchor" href="#arg-gene-ids"></a></dt>
 <dd><p>(<code>character</code>)<br> original gene IDs including prefix and optional
 delimiter before the digits.</p></dd>
 
 
-<dt>prefix</dt>
+<dt id="arg-prefix">prefix<a class="anchor" aria-label="anchor" href="#arg-prefix"></a></dt>
 <dd><p>(<code>string</code>)<br> common prefix to be stripped away from <code>gene_ids</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Character vector that contains only the digits for each gene ID.</p>
+    <p>Character vector that contains only the digits for each gene ID.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -106,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "11185" "10677"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -115,14 +90,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_tech_failure_flag.html b/main/reference/h_tech_failure_flag.html
new file mode 100644
index 00000000..ade2825d
--- /dev/null
+++ b/main/reference/h_tech_failure_flag.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/quality_flags.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/quality_flags.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_tpm.html b/main/reference/h_tpm.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_tpm.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/normalize.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_unique_labels.html b/main/reference/h_unique_labels.html
index 9db3aa33..303ba9a8 100644
--- a/main/reference/h_unique_labels.html
+++ b/main/reference/h_unique_labels.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This helper function generates a set of unique labels given
-unique IDs and not necessarily unique names."><title>Creation of Unique Labels — h_unique_labels • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creation of Unique Labels — h_unique_labels"><meta property="og:description" content="This helper function generates a set of unique labels given
-unique IDs and not necessarily unique names."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Creation of Unique Labels — h_unique_labels • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creation of Unique Labels — h_unique_labels"><meta name="description" content="This helper function generates a set of unique labels given
+unique IDs and not necessarily unique names."><meta property="og:description" content="This helper function generates a set of unique labels given
+unique IDs and not necessarily unique names."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Creation of Unique Labels</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/GeneSpec-class.R" class="external-link"><code>R/GeneSpec-class.R</code></a></small>
       <div class="d-none name"><code>h_unique_labels.Rd</code></div>
     </div>
 
@@ -76,19 +51,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ids</dt>
+
+
+<dl><dt id="arg-ids">ids<a class="anchor" aria-label="anchor" href="#arg-ids"></a></dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> unique IDs.</p></dd>
 
 
-<dt>nms</dt>
+<dt id="arg-nms">nms<a class="anchor" aria-label="anchor" href="#arg-nms"></a></dt>
 <dd><p>(<code>character</code> or <code>NULL</code>)<br> not necessarily unique names if provided.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Character vector where empty names are replaced by the IDs and
+    <p>Character vector where empty names are replaced by the IDs and
 non-unique names are made unique by appending the IDs in parentheses.</p>
     </div>
 
@@ -102,7 +77,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1" "2" "3"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -111,14 +86,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/h_voom.html b/main/reference/h_voom.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_voom.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/normalize.html">
+  </head>
+</html>
+
diff --git a/main/reference/h_vst.html b/main/reference/h_vst.html
new file mode 100644
index 00000000..71f065fc
--- /dev/null
+++ b/main/reference/h_vst.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/normalize.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/normalize.html">
+  </head>
+</html>
+
diff --git a/main/reference/hermes-package.html b/main/reference/hermes-package.html
index 09ac8497..72124e66 100644
--- a/main/reference/hermes-package.html
+++ b/main/reference/hermes-package.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="hermes facilitates preprocessing, analyzing, and reporting of RNA-seq data."><title>hermes Package — hermes-package • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="hermes Package — hermes-package"><meta property="og:description" content="hermes facilitates preprocessing, analyzing, and reporting of RNA-seq data."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>hermes Package — hermes-package • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="hermes Package — hermes-package"><meta name="description" content="hermes facilitates preprocessing, analyzing, and reporting of RNA-seq data."><meta property="og:description" content="hermes facilitates preprocessing, analyzing, and reporting of RNA-seq data."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,55 +7,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>hermes</code> Package</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/package.R" class="external-link"><code>R/package.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/package.R" class="external-link"><code>R/package.R</code></a></small>
       <div class="d-none name"><code>hermes-package.Rd</code></div>
     </div>
 
@@ -93,7 +68,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 </ul><p>Other contributors:</p><ul><li><p>F. Hoffmann-La Roche AG [copyright holder, funder]</p></li>
 </ul></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -102,14 +77,14 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/hermes.html b/main/reference/hermes.html
new file mode 100644
index 00000000..c513a822
--- /dev/null
+++ b/main/reference/hermes.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/hermes-package.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/hermes-package.html">
+  </head>
+</html>
+
diff --git a/main/reference/hermes_data.html b/main/reference/hermes_data.html
index dd63c90e..31eb8315 100644
--- a/main/reference/hermes_data.html
+++ b/main/reference/hermes_data.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Example HermesData Data — hermes_data • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example HermesData Data — hermes_data"><meta name="description" content="
 This example HermesData is created from the underlying SummarizedExperiment::SummarizedExperiment
 object by renaming descriptors to align with standard specification. It already
-contains the required columns in rowData and colData."><title>Example HermesData Data — hermes_data • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example HermesData Data — hermes_data"><meta property="og:description" content="
+contains the required columns in rowData and colData."><meta property="og:description" content="
 This example HermesData is created from the underlying SummarizedExperiment::SummarizedExperiment
 object by renaming descriptors to align with standard specification. It already
-contains the required columns in rowData and colData."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+contains the required columns in rowData and colData."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,61 +13,39 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Example <code>HermesData</code> Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>hermes_data.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#stable" class="external-link"><img src="figures/lifecycle-stable.svg" alt="[Stable]"></a></p>
-<p>This example <code><a href="HermesData-class.html">HermesData</a></code> is created from the underlying <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
+<p>This example <code><a href="HermesData-class.html">HermesData</a></code> is created from the underlying <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
 object by renaming descriptors to align with standard specification. It already
 contains the required columns in <code>rowData</code> and <code>colData</code>.</p>
     </div>
@@ -91,11 +66,11 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="summarized_experiment.html">summarized_experiment</a></code> for the underlying <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
+    <div class="dont-index"><p><code><a href="summarized_experiment.html">summarized_experiment</a></code> for the underlying <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
 object.</p></div>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -104,14 +79,14 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/index.html b/main/reference/index.html
index 4f758fdf..dec149c9 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,609 +7,673 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-index">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Function reference</h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Package index</h1>
     </div>
 
     <div class="section level2">
       <h2 id="package">Package<a class="anchor" aria-label="anchor" href="#package"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="hermes-package.html">hermes</a></code> <code><a href="hermes-package.html">hermes-package</a></code> 
+
+          <code><a href="hermes-package.html">hermes</a></code> <code><a href="hermes-package.html">hermes-package</a></code>
+
         </dt>
         <dd><code>hermes</code> Package</dd>
       </dl></div><div class="section level2">
       <h2 id="classes">Classes<a class="anchor" aria-label="anchor" href="#classes"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="HermesData-class.html">HermesData()</a></code> <code><a href="HermesData-class.html">HermesDataFromMatrix()</a></code> 
+
+          <code><a href="HermesData-class.html">HermesData()</a></code> <code><a href="HermesData-class.html">HermesDataFromMatrix()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>HermesData</code> and <code>RangedHermesData</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="calc_cor.html">correlate(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="calc_cor.html">autoplot(<i>&lt;HermesDataCor&gt;</i>)</a></code> 
+
+          <code><a href="calc_cor.html">correlate(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="calc_cor.html">autoplot(<i>&lt;HermesDataCor&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Correlation between Sample Counts of <code>AnyHermesData</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="calc_pca.html">calc_pca()</a></code> 
+
+          <code><a href="calc_pca.html">calc_pca()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Principal Components Analysis Calculation</dd>
       </dl><dl><dt>
-          
-          <code><a href="top_genes.html">top_genes()</a></code> <code><a href="top_genes.html">autoplot(<i>&lt;HermesDataTopGenes&gt;</i>)</a></code> 
+
+          <code><a href="top_genes.html">top_genes()</a></code> <code><a href="top_genes.html">autoplot(<i>&lt;HermesDataTopGenes&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Derivation of Top Genes</dd>
       </dl><dl><dt>
-          
-          <code><a href="summary.html">summary()</a></code> <code><a href="summary.html">show(<i>&lt;HermesDataSummary&gt;</i>)</a></code> 
+
+          <code><a href="summary.html">summary()</a></code> <code><a href="summary.html">show(<i>&lt;HermesDataSummary&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Summary Method for <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="pca_cor_samplevar.html">correlate(<i>&lt;HermesDataPca&gt;</i>)</a></code> <code><a href="pca_cor_samplevar.html">autoplot(<i>&lt;HermesDataPcaCor&gt;</i>)</a></code> 
+
+          <code><a href="pca_cor_samplevar.html">correlate(<i>&lt;HermesDataPca&gt;</i>)</a></code> <code><a href="pca_cor_samplevar.html">autoplot(<i>&lt;HermesDataPcaCor&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Correlation of Principal Components with Sample Variables</dd>
       </dl><dl><dt>
-          
-          <code><a href="diff_expression.html">diff_expression()</a></code> <code><a href="diff_expression.html">autoplot(<i>&lt;HermesDataDiffExpr&gt;</i>)</a></code> 
+
+          <code><a href="diff_expression.html">diff_expression()</a></code> <code><a href="diff_expression.html">autoplot(<i>&lt;HermesDataDiffExpr&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Differential Expression Analysis</dd>
       </dl><dl><dt>
-          
-          <code><a href="connect_biomart.html">connect_biomart()</a></code> 
+
+          <code><a href="connect_biomart.html">connect_biomart()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Connection to <code>BioMart</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="GeneSpec.html">GeneSpec</a></code> 
+
+          <code><a href="GeneSpec.html">GeneSpec</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>R6 Class Representing a Gene (Signature) Specification</dd>
       </dl></div><div class="section level2">
       <h2 id="constructors">Constructors<a class="anchor" aria-label="anchor" href="#constructors"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="HermesData-class.html">HermesData()</a></code> <code><a href="HermesData-class.html">HermesDataFromMatrix()</a></code> 
+
+          <code><a href="HermesData-class.html">HermesData()</a></code> <code><a href="HermesData-class.html">HermesDataFromMatrix()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>HermesData</code> and <code>RangedHermesData</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="gene_spec.html">gene_spec()</a></code> 
+
+          <code><a href="gene_spec.html">gene_spec()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>GeneSpec</code> Constructor</dd>
       </dl></div><div class="section level2">
       <h2 id="internal-helper-functions">Internal Helper Functions<a class="anchor" aria-label="anchor" href="#internal-helper-functions"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="all_na.html">all_na()</a></code> 
+
+          <code><a href="all_na.html">all_na()</a></code>
+
         </dt>
         <dd>Checks Whether All Missing</dd>
       </dl><dl><dt>
-          
-          <code><a href="cat_with_newline.html">cat_with_newline()</a></code> 
+
+          <code><a href="cat_with_newline.html">cat_with_newline()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Concatenate and Print with Newline</dd>
       </dl><dl><dt>
-          
-          <code><a href="validate.html">validate_counts()</a></code> <code><a href="validate.html">validate_cols()</a></code> <code><a href="validate.html">validate_row_data()</a></code> <code><a href="validate.html">validate_col_data()</a></code> <code><a href="validate.html">validate_names()</a></code> <code><a href="validate.html">validate_prefix()</a></code> 
+
+          <code><a href="validate.html">validate_counts()</a></code> <code><a href="validate.html">validate_cols()</a></code> <code><a href="validate.html">validate_row_data()</a></code> <code><a href="validate.html">validate_col_data()</a></code> <code><a href="validate.html">validate_names()</a></code> <code><a href="validate.html">validate_prefix()</a></code>
+
         </dt>
         <dd>Internal Helper Functions for Validation of <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_map_pos.html">h_map_pos()</a></code> 
+
+          <code><a href="h_map_pos.html">h_map_pos()</a></code>
+
         </dt>
         <dd>Helper Function For Matching Map Values to Names</dd>
       </dl><dl><dt>
-          
-          <code><a href="normalize.html">normalize(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="normalize.html">h_cpm()</a></code> <code><a href="normalize.html">h_rpkm()</a></code> <code><a href="normalize.html">h_tpm()</a></code> <code><a href="normalize.html">h_voom()</a></code> <code><a href="normalize.html">h_vst()</a></code> <code><a href="normalize.html">h_rlog()</a></code> 
+
+          <code><a href="normalize.html">normalize(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="normalize.html">h_cpm()</a></code> <code><a href="normalize.html">h_rpkm()</a></code> <code><a href="normalize.html">h_tpm()</a></code> <code><a href="normalize.html">h_voom()</a></code> <code><a href="normalize.html">h_vst()</a></code> <code><a href="normalize.html">h_rlog()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Normalization of <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="quality_flags.html">add_quality_flags()</a></code> <code><a href="quality_flags.html">h_low_expression_flag()</a></code> <code><a href="quality_flags.html">h_low_depth_flag()</a></code> <code><a href="quality_flags.html">h_tech_failure_flag()</a></code> <code><a href="quality_flags.html">get_tech_failure()</a></code> <code><a href="quality_flags.html">get_low_depth()</a></code> <code><a href="quality_flags.html">get_low_expression()</a></code> 
+
+          <code><a href="quality_flags.html">add_quality_flags()</a></code> <code><a href="quality_flags.html">h_low_expression_flag()</a></code> <code><a href="quality_flags.html">h_low_depth_flag()</a></code> <code><a href="quality_flags.html">h_tech_failure_flag()</a></code> <code><a href="quality_flags.html">get_tech_failure()</a></code> <code><a href="quality_flags.html">get_low_depth()</a></code> <code><a href="quality_flags.html">get_low_expression()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Add Quality Flags</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_diff_expr_voom.html">h_diff_expr_voom()</a></code> 
+
+          <code><a href="h_diff_expr_voom.html">h_diff_expr_voom()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>limma</code>/voom Differential Expression Analysis</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_diff_expr_deseq2.html">h_diff_expr_deseq2()</a></code> 
+
+          <code><a href="h_diff_expr_deseq2.html">h_diff_expr_deseq2()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>DESeq2</code> Differential Expression Analysis</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_pca_var_rsquared.html">h_pca_var_rsquared()</a></code> 
+
+          <code><a href="h_pca_var_rsquared.html">h_pca_var_rsquared()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Calculation of R2 between Sample Variable and Principal Components</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_pca_df_r2_matrix.html">h_pca_df_r2_matrix()</a></code> 
+
+          <code><a href="h_pca_df_r2_matrix.html">h_pca_df_r2_matrix()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Calculation of R2 Matrix between Sample Variables and Principal Components</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_get_annotation_biomart.html">h_get_annotation_biomart()</a></code> 
+
+          <code><a href="h_get_annotation_biomart.html">h_get_annotation_biomart()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Get Annotations from <code>BioMart</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="h_get_granges_by_id.html">h_get_granges_by_id()</a></code> 
+
+          <code><a href="h_get_granges_by_id.html">h_get_granges_by_id()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Conversion of <code>BioMart</code> Coordinates into <code>GRanges</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="h_get_size_biomart.html">h_get_size_biomart()</a></code> 
+
+          <code><a href="h_get_size_biomart.html">h_get_size_biomart()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Total Length of All Exons for Genes</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_ensembl_to_entrez_ids.html">h_ensembl_to_entrez_ids()</a></code> 
+
+          <code><a href="h_ensembl_to_entrez_ids.html">h_ensembl_to_entrez_ids()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Translation of <code>Ensembl</code> to <code>Entrez</code> Gene IDs</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_strip_prefix.html">h_strip_prefix()</a></code> 
+
+          <code><a href="h_strip_prefix.html">h_strip_prefix()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Stripping Prefix from Gene IDs</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_has_req_annotations.html">h_has_req_annotations()</a></code> 
+
+          <code><a href="h_has_req_annotations.html">h_has_req_annotations()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Predicate for Required Annotations</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_short_list.html">h_short_list()</a></code> 
+
+          <code><a href="h_short_list.html">h_short_list()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Make a Short List of a Character Vector</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_parens.html">h_parens()</a></code> 
+
+          <code><a href="h_parens.html">h_parens()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Parenthesize a Character Vector</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_all_duplicated.html">h_all_duplicated()</a></code> 
+
+          <code><a href="h_all_duplicated.html">h_all_duplicated()</a></code>
+
         </dt>
         <dd>Finding All Duplicates in Vector</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_unique_labels.html">h_unique_labels()</a></code> 
+
+          <code><a href="h_unique_labels.html">h_unique_labels()</a></code>
+
         </dt>
         <dd>Creation of Unique Labels</dd>
       </dl><dl><dt>
-          
-          <code><a href="h_df_factors_with_explicit_na.html">h_df_factors_with_explicit_na()</a></code> 
+
+          <code><a href="h_df_factors_with_explicit_na.html">h_df_factors_with_explicit_na()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Conversion to Factors with Explicit Missing Level in a <code>data.frame</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_boxplot.html">draw_boxplot()</a></code> <code><a href="draw_boxplot.html">h_draw_boxplot_df()</a></code> 
+
+          <code><a href="draw_boxplot.html">draw_boxplot()</a></code> <code><a href="draw_boxplot.html">h_draw_boxplot_df()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Boxplot for Gene Expression Values</dd>
       </dl></div><div class="section level2">
       <h2 id="example-data">Example Data<a class="anchor" aria-label="anchor" href="#example-data"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="expression_set.html">expression_set</a></code> 
+
+          <code><a href="expression_set.html">expression_set</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Example <code>ExpressionSet</code> Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="hermes_data.html">hermes_data</a></code> 
+
+          <code><a href="hermes_data.html">hermes_data</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Example <code>HermesData</code> Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="summarized_experiment.html">summarized_experiment</a></code> 
+
+          <code><a href="summarized_experiment.html">summarized_experiment</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Example <code>SummarizedExperiment</code> Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="multi_assay_experiment.html">multi_assay_experiment</a></code> 
+
+          <code><a href="multi_assay_experiment.html">multi_assay_experiment</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Example <code>MultiAssayExperiment</code> Data</dd>
       </dl></div><div class="section level2">
       <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="annotation.html">annotation(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="annotation.html">.row_data_annotation_cols</a></code> <code><a href="annotation.html">`annotation&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;DataFrame&gt;</i>)</a></code> 
+
+          <code><a href="annotation.html">annotation(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="annotation.html">.row_data_annotation_cols</a></code> <code><a href="annotation.html">`annotation&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;DataFrame&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Annotation Accessor and Setter</dd>
       </dl><dl><dt>
-          
-          <code><a href="cbind.html">cbind</a></code> 
+
+          <code><a href="cbind.html">cbind</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Column Binding of <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="correlate.html">correlate()</a></code> 
+
+          <code><a href="correlate.html">correlate()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Generic Function for Correlation Calculations</dd>
       </dl><dl><dt>
-          
-          <code><a href="counts.html">counts(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="counts.html">`counts&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;matrix&gt;</i>)</a></code> 
+
+          <code><a href="counts.html">counts(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="counts.html">`counts&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;matrix&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Counts Accessor and Setter</dd>
       </dl><dl><dt>
-          
-          <code><a href="extra_data_names.html">extraColDataNames()</a></code> <code><a href="extra_data_names.html">extraRowDataNames()</a></code> 
+
+          <code><a href="extra_data_names.html">extraColDataNames()</a></code> <code><a href="extra_data_names.html">extraRowDataNames()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Extra Variable Names Accessor Methods</dd>
       </dl><dl><dt>
-          
-          <code><a href="filter.html">filter()</a></code> 
+
+          <code><a href="filter.html">filter()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Filter <code>AnyHermesData</code> on Subset Passing Default QC Flags</dd>
       </dl><dl><dt>
-          
-          <code><a href="genes.html">genes()</a></code> 
+
+          <code><a href="genes.html">genes()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Gene IDs Accessor</dd>
       </dl><dl><dt>
-          
-          <code><a href="isEmpty.html">isEmpty(<i>&lt;SummarizedExperiment&gt;</i>)</a></code> 
+
+          <code><a href="isEmpty.html">isEmpty(<i>&lt;SummarizedExperiment&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Checking for Empty <code>SummarizedExperiment</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="lapply.html">lapply(<i>&lt;MultiAssayExperiment&gt;</i>)</a></code> 
+
+          <code><a href="lapply.html">lapply(<i>&lt;MultiAssayExperiment&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd><code>lapply</code> method for <code>MultiAssayExperiment</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="metadata.html">metadata</a></code> 
+
+          <code><a href="metadata.html">metadata</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Metadata Accessor and Setter</dd>
       </dl><dl><dt>
-          
-          <code><a href="normalize.html">normalize(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="normalize.html">h_cpm()</a></code> <code><a href="normalize.html">h_rpkm()</a></code> <code><a href="normalize.html">h_tpm()</a></code> <code><a href="normalize.html">h_voom()</a></code> <code><a href="normalize.html">h_vst()</a></code> <code><a href="normalize.html">h_rlog()</a></code> 
+
+          <code><a href="normalize.html">normalize(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="normalize.html">h_cpm()</a></code> <code><a href="normalize.html">h_rpkm()</a></code> <code><a href="normalize.html">h_tpm()</a></code> <code><a href="normalize.html">h_voom()</a></code> <code><a href="normalize.html">h_vst()</a></code> <code><a href="normalize.html">h_rlog()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Normalization of <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="prefix.html">prefix()</a></code> 
+
+          <code><a href="prefix.html">prefix()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Prefix Accessor</dd>
       </dl><dl><dt>
-          
-          <code><a href="query.html">query()</a></code> 
+
+          <code><a href="query.html">query()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Query Gene Annotations from a Connection</dd>
       </dl><dl><dt>
-          
-          <code><a href="rbind.html">rbind</a></code> 
+
+          <code><a href="rbind.html">rbind</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Row Binding of <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="rename.html">rename(<i>&lt;SummarizedExperiment&gt;</i>)</a></code> <code><a href="rename.html">rename(<i>&lt;data.frame&gt;</i>)</a></code> 
+
+          <code><a href="rename.html">rename(<i>&lt;SummarizedExperiment&gt;</i>)</a></code> <code><a href="rename.html">rename(<i>&lt;data.frame&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Renaming Contents of <code>SummarizedExperiment</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="samples.html">samples(<i>&lt;AnyHermesData&gt;</i>)</a></code> 
+
+          <code><a href="samples.html">samples(<i>&lt;AnyHermesData&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Sample IDs Accessor</dd>
       </dl><dl><dt>
-          
-          <code><a href="show.html">show(<i>&lt;HermesData&gt;</i>)</a></code> <code><a href="show.html">show(<i>&lt;RangedHermesData&gt;</i>)</a></code> 
+
+          <code><a href="show.html">show(<i>&lt;HermesData&gt;</i>)</a></code> <code><a href="show.html">show(<i>&lt;RangedHermesData&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Show Method for <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="subset.html">subset</a></code> 
+
+          <code><a href="subset.html">subset</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Subsetting <code>AnyHermesData</code> Objects</dd>
       </dl><dl><dt>
-          
-          <code><a href="summary.html">summary()</a></code> <code><a href="summary.html">show(<i>&lt;HermesDataSummary&gt;</i>)</a></code> 
+
+          <code><a href="summary.html">summary()</a></code> <code><a href="summary.html">show(<i>&lt;HermesDataSummary&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Summary Method for <code>AnyHermesData</code> Objects</dd>
       </dl></div><div class="section level2">
       <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="quality_flags.html">add_quality_flags()</a></code> <code><a href="quality_flags.html">h_low_expression_flag()</a></code> <code><a href="quality_flags.html">h_low_depth_flag()</a></code> <code><a href="quality_flags.html">h_tech_failure_flag()</a></code> <code><a href="quality_flags.html">get_tech_failure()</a></code> <code><a href="quality_flags.html">get_low_depth()</a></code> <code><a href="quality_flags.html">get_low_expression()</a></code> 
+
+          <code><a href="quality_flags.html">add_quality_flags()</a></code> <code><a href="quality_flags.html">h_low_expression_flag()</a></code> <code><a href="quality_flags.html">h_low_depth_flag()</a></code> <code><a href="quality_flags.html">h_tech_failure_flag()</a></code> <code><a href="quality_flags.html">get_tech_failure()</a></code> <code><a href="quality_flags.html">get_low_depth()</a></code> <code><a href="quality_flags.html">get_low_expression()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Add Quality Flags</dd>
       </dl><dl><dt>
-          
-          <code><a href="calc_pca.html">calc_pca()</a></code> 
+
+          <code><a href="calc_pca.html">calc_pca()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Principal Components Analysis Calculation</dd>
       </dl><dl><dt>
-          
-          <code><a href="diff_expression.html">diff_expression()</a></code> <code><a href="diff_expression.html">autoplot(<i>&lt;HermesDataDiffExpr&gt;</i>)</a></code> 
+
+          <code><a href="diff_expression.html">diff_expression()</a></code> <code><a href="diff_expression.html">autoplot(<i>&lt;HermesDataDiffExpr&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Differential Expression Analysis</dd>
       </dl><dl><dt>
-          
-          <code><a href="set_tech_failure.html">set_tech_failure()</a></code> 
+
+          <code><a href="set_tech_failure.html">set_tech_failure()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Set Technical Failure Flags</dd>
       </dl><dl><dt>
-          
-          <code><a href="top_genes.html">top_genes()</a></code> <code><a href="top_genes.html">autoplot(<i>&lt;HermesDataTopGenes&gt;</i>)</a></code> 
+
+          <code><a href="top_genes.html">top_genes()</a></code> <code><a href="top_genes.html">autoplot(<i>&lt;HermesDataTopGenes&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Derivation of Top Genes</dd>
       </dl><dl><dt>
-          
-          <code><a href="connect_biomart.html">connect_biomart()</a></code> 
+
+          <code><a href="connect_biomart.html">connect_biomart()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Connection to <code>BioMart</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="df_cols_to_factor.html">df_cols_to_factor()</a></code> 
+
+          <code><a href="df_cols_to_factor.html">df_cols_to_factor()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Conversion of Eligible Columns to Factor Variables in a <code>DataFrame</code></dd>
       </dl><dl><dt>
-          
-          <code><a href="colPrinComp1.html">colPrinComp1()</a></code> 
+
+          <code><a href="colPrinComp1.html">colPrinComp1()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>First Principal Component (PC1) Gene Signature</dd>
       </dl><dl><dt>
-          
-          <code><a href="colMeanZscores.html">colMeanZscores()</a></code> 
+
+          <code><a href="colMeanZscores.html">colMeanZscores()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Mean Z-score Gene Signature</dd>
       </dl><dl><dt>
-          
-          <code><a href="wrap_in_mae.html">wrap_in_mae()</a></code> 
+
+          <code><a href="wrap_in_mae.html">wrap_in_mae()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Wrap in MAE</dd>
       </dl><dl><dt>
-          
-          <code><a href="col_data_with_genes.html">col_data_with_genes()</a></code> 
+
+          <code><a href="col_data_with_genes.html">col_data_with_genes()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Sample Variables with Selected Gene Information</dd>
       </dl><dl><dt>
-          
-          <code><a href="inner_join_cdisc.html">inner_join_cdisc()</a></code> 
+
+          <code><a href="inner_join_cdisc.html">inner_join_cdisc()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Inner Joining a Genes with a CDISC Data Set</dd>
       </dl><dl><dt>
-          
-          <code><a href="cut_quantile.html">cut_quantile()</a></code> 
+
+          <code><a href="cut_quantile.html">cut_quantile()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Cutting a Numeric Vector into a Factor of Quantile Bins</dd>
       </dl></div><div class="section level2">
       <h2 id="graphs">Graphs<a class="anchor" aria-label="anchor" href="#graphs"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="draw_libsize_hist.html">draw_libsize_hist()</a></code> 
+
+          <code><a href="draw_libsize_hist.html">draw_libsize_hist()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Histogram of Library Sizes</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_libsize_qq.html">draw_libsize_qq()</a></code> 
+
+          <code><a href="draw_libsize_qq.html">draw_libsize_qq()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Q-Q Plot of Library Sizes</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_libsize_densities.html">draw_libsize_densities()</a></code> 
+
+          <code><a href="draw_libsize_densities.html">draw_libsize_densities()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Density Plot of (Log) Counts Distributions</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_nonzero_boxplot.html">draw_nonzero_boxplot()</a></code> 
+
+          <code><a href="draw_nonzero_boxplot.html">draw_nonzero_boxplot()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Boxplot of Non-Zero Genes</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_genes_barplot.html">draw_genes_barplot()</a></code> 
+
+          <code><a href="draw_genes_barplot.html">draw_genes_barplot()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Stacked Barplot of Low Expression Genes by Chromosome</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_heatmap.html">draw_heatmap()</a></code> 
+
+          <code><a href="draw_heatmap.html">draw_heatmap()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Heatmap for Gene Expression Counts</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_scatterplot.html">draw_scatterplot()</a></code> 
+
+          <code><a href="draw_scatterplot.html">draw_scatterplot()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Scatterplot for Gene Expression Values</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_barplot.html">draw_barplot()</a></code> 
+
+          <code><a href="draw_barplot.html">draw_barplot()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Barplot for Gene Expression Percentiles</dd>
       </dl><dl><dt>
-          
-          <code><a href="draw_boxplot.html">draw_boxplot()</a></code> <code><a href="draw_boxplot.html">h_draw_boxplot_df()</a></code> 
+
+          <code><a href="draw_boxplot.html">draw_boxplot()</a></code> <code><a href="draw_boxplot.html">h_draw_boxplot_df()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Boxplot for Gene Expression Values</dd>
       </dl><dl><dt>
-          
-          <code><a href="plot_all.html">autoplot(<i>&lt;AnyHermesData&gt;</i>)</a></code> 
+
+          <code><a href="plot_all.html">autoplot(<i>&lt;AnyHermesData&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>All Standard Plots in Default Setting</dd>
       </dl></div><div class="section level2">
       <h2 id="control-functions">Control Functions<a class="anchor" aria-label="anchor" href="#control-functions"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="control_normalize.html">control_normalize()</a></code> 
+
+          <code><a href="control_normalize.html">control_normalize()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control Settings for Counts Normalization</dd>
       </dl><dl><dt>
-          
-          <code><a href="control_quality.html">control_quality()</a></code> 
+
+          <code><a href="control_quality.html">control_quality()</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Control for Specified Quality Flags</dd>
       </dl></div><div class="section level2">
       <h2 id="assertions">Assertions<a class="anchor" aria-label="anchor" href="#assertions"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="assertion_arguments.html">assertion_arguments</a></code> 
+
+          <code><a href="assertion_arguments.html">assertion_arguments</a></code>
+
         </dt>
         <dd>Standard Assertion Arguments</dd>
       </dl><dl><dt>
-          
-          <code><a href="check_proportion.html">check_proportion()</a></code> <code><a href="check_proportion.html">assert_proportion()</a></code> <code><a href="check_proportion.html">test_proportion()</a></code> <code><a href="check_proportion.html">expect_proportion()</a></code> 
+
+          <code><a href="check_proportion.html">check_proportion()</a></code> <code><a href="check_proportion.html">assert_proportion()</a></code> <code><a href="check_proportion.html">test_proportion()</a></code> <code><a href="check_proportion.html">expect_proportion()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Check for proportion</dd>
       </dl><dl><dt>
-          
-          <code><a href="assertions.html">is_class()</a></code> <code><a href="assertions.html">is_hermes_data()</a></code> <code><a href="assertions.html">is_counts_vector()</a></code> <code><a href="assertions.html">is_list_with()</a></code> <code><a href="assertions.html">one_provided()</a></code> <code><a href="assertions.html">is_constant()</a></code> 
+
+          <code><a href="assertions.html">is_class()</a></code> <code><a href="assertions.html">is_hermes_data()</a></code> <code><a href="assertions.html">is_counts_vector()</a></code> <code><a href="assertions.html">is_list_with()</a></code> <code><a href="assertions.html">one_provided()</a></code> <code><a href="assertions.html">is_constant()</a></code>
+          <span class="badge lifecycle lifecycle-experimental">experimental</span>
         </dt>
         <dd>Additional Assertions for <code>assert_that</code></dd>
       </dl></div><div class="section level2">
       <h2 id="constants">Constants<a class="anchor" aria-label="anchor" href="#constants"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="annotation.html">annotation(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="annotation.html">.row_data_annotation_cols</a></code> <code><a href="annotation.html">`annotation&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;DataFrame&gt;</i>)</a></code> 
+
+          <code><a href="annotation.html">annotation(<i>&lt;AnyHermesData&gt;</i>)</a></code> <code><a href="annotation.html">.row_data_annotation_cols</a></code> <code><a href="annotation.html">`annotation&lt;-`(<i>&lt;AnyHermesData&gt;</i>,<i>&lt;DataFrame&gt;</i>)</a></code>
+          <span class="badge lifecycle lifecycle-stable">stable</span>
         </dt>
         <dd>Annotation Accessor and Setter</dd>
       </dl></div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -621,14 +682,14 @@ <h2 id="constants">Constants<a class="anchor" aria-label="anchor" href="#constan
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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diff --git a/main/reference/inner_join_cdisc.html b/main/reference/inner_join_cdisc.html
index 305a3d5f..41913ebe 100644
--- a/main/reference/inner_join_cdisc.html
+++ b/main/reference/inner_join_cdisc.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-This is a useful function when trying to join genetic with CDISC data sets."><title>Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc"><meta property="og:description" content="
-This is a useful function when trying to join genetic with CDISC data sets."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc"><meta name="description" content="
+This is a useful function when trying to join genetic with CDISC data sets."><meta property="og:description" content="
+This is a useful function when trying to join genetic with CDISC data sets."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Inner Joining a Genes with a CDISC Data Set</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/join_cdisc.R" class="external-link"><code>R/join_cdisc.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/join_cdisc.R" class="external-link"><code>R/join_cdisc.R</code></a></small>
       <div class="d-none name"><code>inner_join_cdisc.Rd</code></div>
     </div>
 
@@ -81,27 +56,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gene_data</dt>
+
+
+<dl><dt id="arg-gene-data">gene_data<a class="anchor" aria-label="anchor" href="#arg-gene-data"></a></dt>
 <dd><p>(<code>data.frame</code> or <code>DataFrame</code>)<br> genetic data.</p></dd>
 
 
-<dt>cdisc_data</dt>
+<dt id="arg-cdisc-data">cdisc_data<a class="anchor" aria-label="anchor" href="#arg-cdisc-data"></a></dt>
 <dd><p>(<code>data.frame</code>)<br> CDISC data (typically patient level data).</p></dd>
 
 
-<dt>patient_key</dt>
+<dt id="arg-patient-key">patient_key<a class="anchor" aria-label="anchor" href="#arg-patient-key"></a></dt>
 <dd><p>(<code>string</code>)<br> patient identifier.</p></dd>
 
 
-<dt>additional_keys</dt>
+<dt id="arg-additional-keys">additional_keys<a class="anchor" aria-label="anchor" href="#arg-additional-keys"></a></dt>
 <dd><p>(<code>character</code>)<br> potential additional keys for the two data sets.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A <code>data.frame</code> which contains columns from both data sets merged by the keys.</p>
+    <p>A <code>data.frame</code> which contains columns from both data sets merged by the keys.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -275,7 +250,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 10      65          FALSE             FALSE         118     7</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -284,14 +259,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/isEmpty.html b/main/reference/isEmpty.html
index faeded19..0c084a3a 100644
--- a/main/reference/isEmpty.html
+++ b/main/reference/isEmpty.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
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-This method checks whether a SummarizedExperiment::SummarizedExperiment object is empty."><title>Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method"><meta property="og:description" content="
-This method checks whether a SummarizedExperiment::SummarizedExperiment object is empty."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method"><meta name="description" content="
+This method checks whether a SummarizedExperiment::SummarizedExperiment object is empty."><meta property="og:description" content="
+This method checks whether a SummarizedExperiment::SummarizedExperiment object is empty."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Checking for Empty <code>SummarizedExperiment</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>isEmpty.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental" class="external-link"><img src="figures/lifecycle-experimental.svg" alt="[Experimental]"></a></p>
-<p>This method checks whether a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object is empty.</p>
+<p>This method checks whether a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object is empty.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for SummarizedExperiment</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'SummarizedExperiment'</span></span>
 <span><span class="fu">isEmpty</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>SummarizedExperiment</code>)<br> object to check.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>Flag whether the <code>object</code> is empty.</p>
+    <p>Flag whether the <code>object</code> is empty.</p>
     </div>
 
     <div class="section level2">
@@ -98,7 +73,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -107,14 +82,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
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diff --git a/main/reference/is_class.html b/main/reference/is_class.html
new file mode 100644
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--- /dev/null
+++ b/main/reference/is_class.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/assertions.html" />
+    <meta name="robots" content="noindex">
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+
diff --git a/main/reference/is_constant.html b/main/reference/is_constant.html
new file mode 100644
index 00000000..7e04746c
--- /dev/null
+++ b/main/reference/is_constant.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/assertions.html" />
+    <meta name="robots" content="noindex">
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+
diff --git a/main/reference/is_counts_vector.html b/main/reference/is_counts_vector.html
new file mode 100644
index 00000000..7e04746c
--- /dev/null
+++ b/main/reference/is_counts_vector.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
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+
diff --git a/main/reference/is_hermes_data.html b/main/reference/is_hermes_data.html
new file mode 100644
index 00000000..7e04746c
--- /dev/null
+++ b/main/reference/is_hermes_data.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
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diff --git a/main/reference/is_list_with.html b/main/reference/is_list_with.html
new file mode 100644
index 00000000..7e04746c
--- /dev/null
+++ b/main/reference/is_list_with.html
@@ -0,0 +1,8 @@
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diff --git a/main/reference/lapply.html b/main/reference/lapply.html
index d602053e..afc92cde 100644
--- a/main/reference/lapply.html
+++ b/main/reference/lapply.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
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-Apply a function on all experiments in an MAE."><title>lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method"><meta property="og:description" content="
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method"><meta name="description" content="
+Apply a function on all experiments in an MAE."><meta property="og:description" content="
+Apply a function on all experiments in an MAE."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1><code>lapply</code> method for <code>MultiAssayExperiment</code></h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>lapply.Rd</code></div>
     </div>
 
@@ -71,34 +46,34 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for MultiAssayExperiment</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'MultiAssayExperiment'</span></span>
 <span><span class="fu">lapply</span><span class="op">(</span><span class="va">X</span>, <span class="va">FUN</span>, safe <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>X</dt>
+
+
+<dl><dt id="arg-x">X<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>MultiAssayExperiment</code>)<br> input.</p></dd>
 
 
-<dt>FUN</dt>
+<dt id="arg-fun">FUN<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
 <dd><p>(<code>function</code>) to be applied to each experiment in <code>X</code>.</p></dd>
 
 
-<dt>safe</dt>
+<dt id="arg-safe">safe<a class="anchor" aria-label="anchor" href="#arg-safe"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether this method should skip experiments
 where the function fails.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments passed to <code>FUN</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>MultiAssayExperiment</code> object with specified function applied.</p>
+    <p><code>MultiAssayExperiment</code> object with specified function applied.</p>
     </div>
 
     <div class="section level2">
@@ -118,7 +93,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">lapply</span><span class="op">(</span><span class="va">object</span>, <span class="va">HermesData</span>, safe <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -127,14 +102,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/main/reference/metadata.html b/main/reference/metadata.html
index e0f88554..7a831bc8 100644
--- a/main/reference/metadata.html
+++ b/main/reference/metadata.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-These methods access or set the metadata in a AnyHermesData object."><title>Metadata Accessor and Setter — metadata • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Metadata Accessor and Setter — metadata"><meta property="og:description" content="
-These methods access or set the metadata in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Metadata Accessor and Setter — metadata • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Metadata Accessor and Setter — metadata"><meta name="description" content="
+These methods access or set the metadata in a AnyHermesData object."><meta property="og:description" content="
+These methods access or set the metadata in a AnyHermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -12,55 +9,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Metadata Accessor and Setter</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>metadata.Rd</code></div>
     </div>
 
@@ -72,19 +47,19 @@
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to access the metadata from.</p></dd>
 
 
-<dt>value</dt>
+<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt>
 <dd><p>(<code>list</code>)<br> the list to replace the current metadata with.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The metadata which is a list.</p>
+    <p>The metadata which is a list.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -103,7 +78,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +87,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
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+
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diff --git a/main/reference/multi_assay_experiment.html b/main/reference/multi_assay_experiment.html
index 8327150b..63dfc4ec 100644
--- a/main/reference/multi_assay_experiment.html
+++ b/main/reference/multi_assay_experiment.html
@@ -1,10 +1,7 @@
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-This example MultiAssayExperiment::MultiAssayExperiment can be used as test data."><title>Example MultiAssayExperiment Data — multi_assay_experiment • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example MultiAssayExperiment Data — multi_assay_experiment"><meta property="og:description" content="
-This example MultiAssayExperiment::MultiAssayExperiment can be used as test data."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Example MultiAssayExperiment Data — multi_assay_experiment • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example MultiAssayExperiment Data — multi_assay_experiment"><meta name="description" content="
+This example MultiAssayExperiment::MultiAssayExperiment can be used as test data."><meta property="og:description" content="
+This example MultiAssayExperiment::MultiAssayExperiment can be used as test data."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
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   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Example <code>MultiAssayExperiment</code> Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>multi_assay_experiment.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental" class="external-link"><img src="figures/lifecycle-experimental.svg" alt="[Experimental]"></a></p>
-<p>This example <code><a href="http://waldronlab.io/MultiAssayExperiment/reference/MultiAssayExperiment.html" class="external-link">MultiAssayExperiment::MultiAssayExperiment</a></code> can be used as test data.</p>
+<p>This example <code><a href="https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html" class="external-link">MultiAssayExperiment::MultiAssayExperiment</a></code> can be used as test data.</p>
     </div>
 
     <div class="section level2">
@@ -76,7 +51,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <code><a href="http://waldronlab.io/MultiAssayExperiment/reference/MultiAssayExperiment.html" class="external-link">MultiAssayExperiment::MultiAssayExperiment</a></code> object with 3 separate <code><a href="HermesData-class.html">HermesData</a></code>
+    <p>A <code><a href="https://github.com/waldronlab/MultiAssayExperiment/reference/MultiAssayExperiment.html" class="external-link">MultiAssayExperiment::MultiAssayExperiment</a></code> object with 3 separate <code><a href="HermesData-class.html">HermesData</a></code>
 objects.</p><ul><li><p>The first object contains 5 samples and covers 1000 features (<code>Entrez</code> gene IDs).</p></li>
 <li><p>The second object contains 9 samples with 2500 features.</p></li>
 <li><p>The third object contains 6 samples with 1300 features.</p></li>
@@ -86,7 +61,7 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
     <p>This is an artificial dataset designed to resemble real data.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -95,14 +70,14 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/normalize.html b/main/reference/normalize.html
index bdbbd82b..7e4c4def 100644
--- a/main/reference/normalize.html
+++ b/main/reference/normalize.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Normalization of AnyHermesData Objects — normalize,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Normalization of AnyHermesData Objects — normalize,AnyHermesData-method"><meta name="description" content="
 The normalize() method is normalizing the input AnyHermesData according to one or more
 specified normalization methods. The results are saved as additional assays
 in the object.
@@ -23,7 +23,7 @@
 count data for all genes into approximately homoskedastic values (having constant variance).
 rlog: The transformation to the log2 scale values with approximately homoskedastic values.
 
-"><title>Normalization of AnyHermesData Objects — normalize,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Normalization of AnyHermesData Objects — normalize,AnyHermesData-method"><meta property="og:description" content="
+"><meta property="og:description" content="
 The normalize() method is normalizing the input AnyHermesData according to one or more
 specified normalization methods. The results are saved as additional assays
 in the object.
@@ -47,10 +47,7 @@
 count data for all genes into approximately homoskedastic values (having constant variance).
 rlog: The transformation to the log2 scale values with approximately homoskedastic values.
 
-"><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -58,55 +55,33 @@
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Normalization of <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/normalization.R" class="external-link"><code>R/normalization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/normalization.R" class="external-link"><code>R/normalization.R</code></a></small>
       <div class="d-none name"><code>normalize.Rd</code></div>
     </div>
 
@@ -137,7 +112,7 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">normalize</span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  methods <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cpm"</span>, <span class="st">"rpkm"</span>, <span class="st">"tpm"</span>, <span class="st">"voom"</span>, <span class="st">"vst"</span><span class="op">)</span>,</span>
@@ -160,32 +135,32 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to normalize.</p></dd>
 
 
-<dt>methods</dt>
+<dt id="arg-methods">methods<a class="anchor" aria-label="anchor" href="#arg-methods"></a></dt>
 <dd><p>(<code>character</code>)<br> which normalization methods to use, see details.</p></dd>
 
 
-<dt>control</dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
 <dd><p>(named <code>list</code>)<br> settings produced by <code><a href="control_normalize.html">control_normalize()</a></code>.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>not used.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code><a href="HermesData-class.html">AnyHermesData</a></code> object with additional assays containing the normalized counts.
+    <p>The <code><a href="HermesData-class.html">AnyHermesData</a></code> object with additional assays containing the normalized counts.
 The <code>control</code> is saved in the <code>metadata</code> of the object for future reference.</p>
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>h_cpm()</code>: calculates the Counts per Million (<code>CPM</code>) normalized counts.</p></li>
 <li><p><code>h_rpkm()</code>: calculates the Reads per Kilobase per Million (RPKM) normalized counts.</p></li>
 <li><p><code>h_tpm()</code>: calculates the Transcripts per Million (TPM) normalized counts.</p></li>
@@ -273,7 +248,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>  - attr(*, "intercept")= num [1:5085, 1] 5.26 8.49 -Inf -Inf -Inf ...</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -282,14 +257,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/one_provided.html b/main/reference/one_provided.html
new file mode 100644
index 00000000..7e04746c
--- /dev/null
+++ b/main/reference/one_provided.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/assertions.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/assertions.html">
+  </head>
+</html>
+
diff --git a/main/reference/pca_cor_samplevar.html b/main/reference/pca_cor_samplevar.html
index c945d263..96e54d03 100644
--- a/main/reference/pca_cor_samplevar.html
+++ b/main/reference/pca_cor_samplevar.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method"><meta name="description" content="
 This correlate() method analyses the correlations (in R2 values) between all sample variables
 in a AnyHermesData object and the principal components of the samples.
-A corresponding autoplot() method then can visualize the results in a heatmap."><title>Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method"><meta property="og:description" content="
+A corresponding autoplot() method then can visualize the results in a heatmap."><meta property="og:description" content="
 This correlate() method analyses the correlations (in R2 values) between all sample variables
 in a AnyHermesData object and the principal components of the samples.
-A corresponding autoplot() method then can visualize the results in a heatmap."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+A corresponding autoplot() method then can visualize the results in a heatmap."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-<li class="nav-item">
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-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
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-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Correlation of Principal Components with Sample Variables</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/pca_cor_samplevar.R" class="external-link"><code>R/pca_cor_samplevar.R</code></a></small>
       <div class="d-none name"><code>pca_cor_samplevar.Rd</code></div>
     </div>
 
@@ -77,10 +52,10 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for HermesDataPca</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'HermesDataPca'</span></span>
 <span><span class="fu"><a href="correlate.html">correlate</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">data</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for HermesDataPcaCor</span></span>
+<span><span class="co"># S4 method for class 'HermesDataPcaCor'</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  cor_colors <span class="op">=</span> <span class="fu">circlize</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/circlize/man/colorRamp2.html" class="external-link">colorRamp2</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"blue"</span>, <span class="st">"white"</span>, <span class="st">"red"</span><span class="op">)</span><span class="op">)</span>,</span>
@@ -90,33 +65,33 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>HermesDataPca</code>)<br> input. It can be generated using <code><a href="calc_pca.html">calc_pca()</a></code> function
 on <code><a href="HermesData-class.html">AnyHermesData</a></code>.</p></dd>
 
 
-<dt>data</dt>
+<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input that was used originally for the PCA.</p></dd>
 
 
-<dt>cor_colors</dt>
+<dt id="arg-cor-colors">cor_colors<a class="anchor" aria-label="anchor" href="#arg-cor-colors"></a></dt>
 <dd><p>(<code>function</code>)<br> color scale function for the correlation values in the heatmap,
 produced by <code><a href="https://rdrr.io/pkg/circlize/man/colorRamp2.html" class="external-link">circlize::colorRamp2()</a></code>.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other arguments to be passed to <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap()</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A <code>HermesDataPcaCor</code> object with R2 values for all sample variables.</p>
+    <p>A <code>HermesDataPcaCor</code> object with R2 values for all sample variables.</p>
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>autoplot(HermesDataPcaCor)</code>: This plot method uses the <code><a href="https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html" class="external-link">ComplexHeatmap::Heatmap()</a></code> function
 to visualize a <code>HermesDataPcaCor</code> object.</p></li>
 </ul></div>
@@ -155,7 +130,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="pca_cor_samplevar-3.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -164,14 +139,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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   </body></html>
 
diff --git a/main/reference/pipe.html b/main/reference/pipe.html
index b43e02f3..2ed31b11 100644
--- a/main/reference/pipe.html
+++ b/main/reference/pipe.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-See magrittr::%&amp;gt;% for details."><title>Pipe operator — %&gt;% • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pipe operator — %&gt;%"><meta property="og:description" content="
-See magrittr::%&amp;gt;% for details."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Pipe operator — %&gt;% • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pipe operator — %&gt;%"><meta name="description" content="
+See magrittr::%&amp;gt;% for details."><meta property="og:description" content="
+See magrittr::%&amp;gt;% for details."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Pipe operator</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>pipe.Rd</code></div>
     </div>
 
@@ -76,9 +51,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The result of the corresponding function call.</p>
+    <p>The result of the corresponding function call.</p>
     </div>
 
     <div class="section level2">
@@ -97,7 +70,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> - Samples with too low depth or technical failures (0):</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -106,14 +79,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/plot_all-1.png b/main/reference/plot_all-1.png
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diff --git a/main/reference/plot_all.html b/main/reference/plot_all.html
index 44734286..2686bf31 100644
--- a/main/reference/plot_all.html
+++ b/main/reference/plot_all.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>All Standard Plots in Default Setting — autoplot,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="All Standard Plots in Default Setting — autoplot,AnyHermesData-method"><meta name="description" content="
 This generates all standard plots - histogram and q-q plot of library sizes, density plot of the (log) counts
 distributions, boxplot of the number of number of non-zero expressed genes per sample, and a stacked barplot of low
-expression genes by chromosome at default setting."><title>All Standard Plots in Default Setting — autoplot,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="All Standard Plots in Default Setting — autoplot,AnyHermesData-method"><meta property="og:description" content="
+expression genes by chromosome at default setting."><meta property="og:description" content="
 This generates all standard plots - histogram and q-q plot of library sizes, density plot of the (log) counts
 distributions, boxplot of the number of number of non-zero expressed genes per sample, and a stacked barplot of low
-expression genes by chromosome at default setting."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+expression genes by chromosome at default setting."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,55 +13,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>All Standard Plots in Default Setting</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/graphs.R" class="external-link"><code>R/graphs.R</code></a></small>
       <div class="d-none name"><code>plot_all.Rd</code></div>
     </div>
 
@@ -77,25 +52,23 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list with the <code>ggplot</code> objects from <code><a href="draw_libsize_hist.html">draw_libsize_hist()</a></code>, <code><a href="draw_libsize_qq.html">draw_libsize_qq()</a></code>,
-<code><a href="draw_libsize_densities.html">draw_libsize_densities()</a></code>, <code><a href="draw_nonzero_boxplot.html">draw_nonzero_boxplot()</a></code> and <code><a href="draw_genes_barplot.html">draw_genes_barplot()</a></code></p>
-
-
-<p>functions with default settings.</p>
+    <p>A list with the <code>ggplot</code> objects from <code><a href="draw_libsize_hist.html">draw_libsize_hist()</a></code>, <code><a href="draw_libsize_qq.html">draw_libsize_qq()</a></code>,
+<code><a href="draw_libsize_densities.html">draw_libsize_densities()</a></code>, <code><a href="draw_nonzero_boxplot.html">draw_nonzero_boxplot()</a></code> and <code><a href="draw_genes_barplot.html">draw_genes_barplot()</a></code>
+functions with default settings.</p>
     </div>
 
     <div class="section level2">
@@ -109,7 +82,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="plot_all-5.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -118,14 +91,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/prefix.html b/main/reference/prefix.html
index e5c4fb01..6c01a15c 100644
--- a/main/reference/prefix.html
+++ b/main/reference/prefix.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-Generic function to access the prefix from an object."><title>Prefix Accessor — prefix • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prefix Accessor — prefix"><meta property="og:description" content="
-Generic function to access the prefix from an object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Prefix Accessor — prefix • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prefix Accessor — prefix"><meta name="description" content="
+Generic function to access the prefix from an object."><meta property="og:description" content="
+Generic function to access the prefix from an object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Prefix Accessor</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>prefix.Rd</code></div>
     </div>
 
@@ -76,19 +51,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code>prefix</code> slot contents.</p>
+    <p>The <code>prefix</code> slot contents.</p>
     </div>
 
     <div class="section level2">
@@ -98,7 +73,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "GeneID"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -107,14 +82,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/quality_flags.html b/main/reference/quality_flags.html
index 1c9f5be5..5fcfb758 100644
--- a/main/reference/quality_flags.html
+++ b/main/reference/quality_flags.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Add Quality Flags — add_quality_flags • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add Quality Flags — add_quality_flags"><meta name="description" content="
 The function add_quality_flags() adds quality flag information to a AnyHermesData object:
 low_expression_flag: for each gene, counts how many samples don't pass a minimum
 expression Counts per Million (CPM) threshold. If too many, then it flags this gene
@@ -13,7 +13,7 @@
 
 
 Separate helper functions are internally used to create the flags, and
-separate getter functions allow easy access to the quality control flags in an object."><title>Add Quality Flags — add_quality_flags • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add Quality Flags — add_quality_flags"><meta property="og:description" content="
+separate getter functions allow easy access to the quality control flags in an object."><meta property="og:description" content="
 The function add_quality_flags() adds quality flag information to a AnyHermesData object:
 low_expression_flag: for each gene, counts how many samples don't pass a minimum
 expression Counts per Million (CPM) threshold. If too many, then it flags this gene
@@ -27,10 +27,7 @@
 
 
 Separate helper functions are internally used to create the flags, and
-separate getter functions allow easy access to the quality control flags in an object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -38,55 +35,33 @@
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Add Quality Flags</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
       <div class="d-none name"><code>quality_flags.Rd</code></div>
     </div>
 
@@ -124,24 +99,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>) <br> input.</p></dd>
 
 
-<dt>control</dt>
+<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt>
 <dd><p>(<code>list</code>) <br> list of settings (thresholds etc.) used to compute the
 quality control flags, produced by <code><a href="control_quality.html">control_quality()</a></code>.</p></dd>
 
 
-<dt>overwrite</dt>
+<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether previously added flags may be overwritten.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The input object with added quality flags.</p>
+    <p>The input object with added quality flags.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -152,7 +127,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>h_low_expression_flag()</code>: creates the low expression flag for genes
 given control settings.</p></li>
 <li><p><code>h_low_depth_flag()</code>: creates the low depth (library size) flag for samples
@@ -248,7 +223,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>             TRUE             TRUE </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -257,14 +232,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/query,character,ConnectionBiomart-method.html b/main/reference/query,character,ConnectionBiomart-method.html
new file mode 100644
index 00000000..691a1e6c
--- /dev/null
+++ b/main/reference/query,character,ConnectionBiomart-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/query.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/query.html">
+  </head>
+</html>
+
diff --git a/main/reference/query.html b/main/reference/query.html
index 404e243b..1a22f828 100644
--- a/main/reference/query.html
+++ b/main/reference/query.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Query Gene Annotations from a Connection — query • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Query Gene Annotations from a Connection — query"><meta name="description" content="
 The generic function query() is the interface for querying gene annotations from
-a data base connection."><title>Query Gene Annotations from a Connection — query • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Query Gene Annotations from a Connection — query"><meta property="og:description" content="
+a data base connection."><meta property="og:description" content="
 The generic function query() is the interface for querying gene annotations from
-a data base connection."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -14,55 +11,33 @@
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Query Gene Annotations from a Connection</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/connections.R" class="external-link"><code>R/connections.R</code></a></small>
       <div class="d-none name"><code>query.Rd</code></div>
     </div>
 
@@ -76,32 +51,32 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">query</span><span class="op">(</span><span class="va">genes</span>, <span class="va">connection</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for character,ConnectionBiomart</span></span>
+<span><span class="co"># S4 method for class 'character,ConnectionBiomart'</span></span>
 <span><span class="fu">query</span><span class="op">(</span><span class="va">genes</span>, <span class="va">connection</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>genes</dt>
+
+
+<dl><dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(<code>character</code>)<br> gene IDs.</p></dd>
 
 
-<dt>connection</dt>
+<dt id="arg-connection">connection<a class="anchor" aria-label="anchor" href="#arg-connection"></a></dt>
 <dd><p>(connection class)<br> data base connection object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A <code><a href="https://rdrr.io/pkg/S4Vectors/man/DataFrame-class.html" class="external-link">S4Vectors::DataFrame</a></code> with the gene annotations. It is required that:</p><ul><li><p>The <code>rownames</code> are identical to the input <code>genes</code>.</p></li>
+    <p>A <code><a href="https://rdrr.io/pkg/S4Vectors/man/DataFrame-class.html" class="external-link">S4Vectors::DataFrame</a></code> with the gene annotations. It is required that:</p><ul><li><p>The <code>rownames</code> are identical to the input <code>genes</code>.</p></li>
 <li><p>The <code>colnames</code> are equal to the annotation columns <code><a href="annotation.html">.row_data_annotation_cols</a></code>.</p></li>
 <li><p>Therefore, missing information needs to be properly included in the <code>DataFrame</code>
 with <code>NA</code> entries.</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>A method is provided for the <code><a href="connect_biomart.html">ConnectionBiomart</a></code> class. However, the framework
 is extensible: It is simple to add new connections and corresponding query methods
 for other data bases, e.g. company internal data bases. Please make sure to
@@ -121,7 +96,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -130,14 +105,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/rbind.html b/main/reference/rbind.html
index e2977b77..96649dee 100644
--- a/main/reference/rbind.html
+++ b/main/reference/rbind.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Row Binding of AnyHermesData Objects — rbind • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Row Binding of AnyHermesData Objects — rbind"><meta name="description" content="
 This method combines AnyHermesData objects with the same samples but different
-features of interest (rows in assays)."><title>Row Binding of AnyHermesData Objects — rbind • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Row Binding of AnyHermesData Objects — rbind"><meta property="og:description" content="
+features of interest (rows in assays)."><meta property="og:description" content="
 This method combines AnyHermesData objects with the same samples but different
-features of interest (rows in assays)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+features of interest (rows in assays)."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,55 +11,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Row Binding of <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>rbind.Rd</code></div>
     </div>
 
@@ -75,24 +50,24 @@
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>...</dt>
+
+
+<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> objects to row bind.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The combined <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
+    <p>The combined <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
-    
+
 <ul><li><p>Note that this just inherits
 <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::rbind,SummarizedExperiment-method()</a></code>. When binding a
-<code><a href="HermesData-class.html">AnyHermesData</a></code> object with a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
+<code><a href="HermesData-class.html">AnyHermesData</a></code> object with a <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>
 object, then the result will be a
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object (the more general
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object (the more general
 class).</p></li>
 <li><p>Note that we need to have unique gene IDs (row names) and the same prefix
 across the combined object.</p></li>
@@ -113,7 +88,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "hermes"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -122,14 +97,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/rename,data.frame-method.html b/main/reference/rename,data.frame-method.html
new file mode 100644
index 00000000..bc54544e
--- /dev/null
+++ b/main/reference/rename,data.frame-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/rename.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/rename.html">
+  </head>
+</html>
+
diff --git a/main/reference/rename.html b/main/reference/rename.html
index 4c291c6a..57e2cbe3 100644
--- a/main/reference/rename.html
+++ b/main/reference/rename.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method"><meta name="description" content="
 This method renames columns of the rowData and colData, as well as assays, of
 SummarizedExperiment::SummarizedExperiment objects. This increases the flexibility
-since renaming can be done before conversion to a HermesData object."><title>Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method"><meta property="og:description" content="
+since renaming can be done before conversion to a HermesData object."><meta property="og:description" content="
 This method renames columns of the rowData and colData, as well as assays, of
 SummarizedExperiment::SummarizedExperiment objects. This increases the flexibility
-since renaming can be done before conversion to a HermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+since renaming can be done before conversion to a HermesData object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
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 </script></head><body>
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+
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Renaming Contents of <code>SummarizedExperiment</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/dplyr_compatibility.R" class="external-link"><code>R/dplyr_compatibility.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a>, <a href="https://github.com/insightsengineering/hermes/blob/main/R/dplyr_compatibility.R" class="external-link"><code>R/dplyr_compatibility.R</code></a></small>
       <div class="d-none name"><code>rename.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental" class="external-link"><img src="figures/lifecycle-experimental.svg" alt="[Experimental]"></a></p>
 <p>This method renames columns of the <code>rowData</code> and <code>colData</code>, as well as assays, of
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> objects. This increases the flexibility
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> objects. This increases the flexibility
 since renaming can be done before conversion to a <code><a href="HermesData-class.html">HermesData</a></code> object.</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for SummarizedExperiment</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'SummarizedExperiment'</span></span>
 <span><span class="fu">rename</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  row_data <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></span><span class="op">(</span><span class="op">)</span>,</span>
@@ -86,40 +61,40 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for data.frame</span></span>
+<span><span class="co"># S4 method for class 'data.frame'</span></span>
 <span><span class="fu">rename</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>SummarizedExperiment</code>)<br> object to rename contents in.</p></dd>
 
 
-<dt>row_data</dt>
+<dt id="arg-row-data">row_data<a class="anchor" aria-label="anchor" href="#arg-row-data"></a></dt>
 <dd><p>(named <code>character</code>)<br> mapping from existing (right-hand side values)
 to new (left-hand side names) column names of <code>rowData</code>.</p></dd>
 
 
-<dt>col_data</dt>
+<dt id="arg-col-data">col_data<a class="anchor" aria-label="anchor" href="#arg-col-data"></a></dt>
 <dd><p>(named <code>character</code>)<br> mapping from existing (right-hand side values)
 to new (left-hand side names) column names of <code>colData</code>.</p></dd>
 
 
-<dt>assays</dt>
+<dt id="arg-assays">assays<a class="anchor" aria-label="anchor" href="#arg-assays"></a></dt>
 <dd><p>(named <code>character</code>)<br> mapping from existing (right-hand side values)
 to new (left-hand side names) assay names.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>additional arguments (not used here).</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object with renamed contents.</p>
+    <p>The <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> object with renamed contents.</p>
     </div>
 
     <div class="section level2">
@@ -146,7 +121,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "counts"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -155,14 +130,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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diff --git a/main/reference/samples.html b/main/reference/samples.html
index 31ca1854..5d196044 100644
--- a/main/reference/samples.html
+++ b/main/reference/samples.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Sample IDs Accessor — samples,AnyHermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample IDs Accessor — samples,AnyHermesData-method"><meta name="description" content="
 Access the sample IDs, i.e. col names, of a AnyHermesData object with a
-nicely named accessor method."><title>Sample IDs Accessor — samples,AnyHermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample IDs Accessor — samples,AnyHermesData-method"><meta property="og:description" content="
+nicely named accessor method."><meta property="og:description" content="
 Access the sample IDs, i.e. col names, of a AnyHermesData object with a
-nicely named accessor method."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Sample IDs Accessor</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>samples.Rd</code></div>
     </div>
 
@@ -74,21 +49,21 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for AnyHermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">samples</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The character vector with the sample IDs.</p>
+    <p>The character vector with the sample IDs.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -106,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [17] "06520023C0018R" "06520099B0017R" "06520015C0016R" "06520019C0023R"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -115,14 +90,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/set_tech_failure.html b/main/reference/set_tech_failure.html
index cc48ac3a..73d07d5e 100644
--- a/main/reference/set_tech_failure.html
+++ b/main/reference/set_tech_failure.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-Setter function which allows the user to define a sample manually as a technical failure."><title>Set Technical Failure Flags — set_tech_failure • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set Technical Failure Flags — set_tech_failure"><meta property="og:description" content="
-Setter function which allows the user to define a sample manually as a technical failure."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Set Technical Failure Flags — set_tech_failure • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set Technical Failure Flags — set_tech_failure"><meta name="description" content="
+Setter function which allows the user to define a sample manually as a technical failure."><meta property="og:description" content="
+Setter function which allows the user to define a sample manually as a technical failure."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,55 +9,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Set Technical Failure Flags</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/quality.R" class="external-link"><code>R/quality.R</code></a></small>
       <div class="d-none name"><code>set_tech_failure.Rd</code></div>
     </div>
 
@@ -76,19 +51,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 
-<dt>sample_ids</dt>
+<dt id="arg-sample-ids">sample_ids<a class="anchor" aria-label="anchor" href="#arg-sample-ids"></a></dt>
 <dd><p>(<code>character</code>) <br> sample IDs to be flagged as technical failures.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code><a href="HermesData-class.html">AnyHermesData</a></code> object with modified technical failure flags.</p>
+    <p><code><a href="HermesData-class.html">AnyHermesData</a></code> object with modified technical failure flags.</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -109,7 +84,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>           TRUE </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -118,14 +93,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/show,HermesDataSummary-method.html b/main/reference/show,HermesDataSummary-method.html
new file mode 100644
index 00000000..95206edb
--- /dev/null
+++ b/main/reference/show,HermesDataSummary-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/summary.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/summary.html">
+  </head>
+</html>
+
diff --git a/main/reference/show,RangedHermesData-method.html b/main/reference/show,RangedHermesData-method.html
new file mode 100644
index 00000000..52927eb5
--- /dev/null
+++ b/main/reference/show,RangedHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/show.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/show.html">
+  </head>
+</html>
+
diff --git a/main/reference/show.html b/main/reference/show.html
index 1769334e..fea39444 100644
--- a/main/reference/show.html
+++ b/main/reference/show.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
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-A show method that displays high-level information of AnyHermesData objects."><title>Show Method for AnyHermesData Objects — show,HermesData-method • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Show Method for AnyHermesData Objects — show,HermesData-method"><meta property="og:description" content="
-A show method that displays high-level information of AnyHermesData objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Show Method for AnyHermesData Objects — show,HermesData-method • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Show Method for AnyHermesData Objects — show,HermesData-method"><meta name="description" content="
+A show method that displays high-level information of AnyHermesData objects."><meta property="og:description" content="
+A show method that displays high-level information of AnyHermesData objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Show Method for <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>show.Rd</code></div>
     </div>
 
@@ -71,31 +46,31 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for HermesData</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'HermesData'</span></span>
 <span><span class="fu">show</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for RangedHermesData</span></span>
+<span><span class="co"># S4 method for class 'RangedHermesData'</span></span>
 <span><span class="fu">show</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> input.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>None (invisible <code>NULL</code>), only used for the side effect of printing to
+    <p>None (invisible <code>NULL</code>), only used for the side effect of printing to
 the console.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     <p>The same method is used for both <code><a href="HermesData-class.html">HermesData</a></code> and <code><a href="HermesData-class.html">RangedHermesData</a></code>
 objects. We need to define this separately to have this method used instead of
-the one inherited from <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p>
+the one inherited from <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code>.</p>
     </div>
 
     <div class="section level2">
@@ -111,7 +86,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> additional sample information(72): Filename SampleID ... TTYPE STDSSDY</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -120,14 +95,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/subset.html b/main/reference/subset.html
index 39cc62bc..19af4983 100644
--- a/main/reference/subset.html
+++ b/main/reference/subset.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subsetting AnyHermesData Objects — subset • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subsetting AnyHermesData Objects — subset"><meta name="description" content="
 This method subsets AnyHermesData objects, based on expressions involving the
-rowData columns and the colData columns."><title>Subsetting AnyHermesData Objects — subset • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subsetting AnyHermesData Objects — subset"><meta property="og:description" content="
+rowData columns and the colData columns."><meta property="og:description" content="
 This method subsets AnyHermesData objects, based on expressions involving the
-rowData columns and the colData columns."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+rowData columns and the colData columns."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
-  </a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Subsetting <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>subset.Rd</code></div>
     </div>
 
@@ -75,25 +50,25 @@
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>AnyHermesData</code>)<br> object to subset from.</p></dd>
 
 
-<dt>subset</dt>
+<dt id="arg-subset">subset<a class="anchor" aria-label="anchor" href="#arg-subset"></a></dt>
 <dd><p>(<code>expression</code>)<br> logical expression based on the <code>rowData</code> columns to
 select genes.</p></dd>
 
 
-<dt>select</dt>
+<dt id="arg-select">select<a class="anchor" aria-label="anchor" href="#arg-select"></a></dt>
 <dd><p>(<code>expression</code>)<br> logical expression based on the <code>colData</code> columns to
 select samples.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The subsetted <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
+    <p>The subsetted <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p>
     </div>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
@@ -144,7 +119,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> additional sample information(72): Filename SampleID ... TTYPE STDSSDY</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -153,14 +128,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/summarized_experiment.html b/main/reference/summarized_experiment.html
index 88250e54..878f21f2 100644
--- a/main/reference/summarized_experiment.html
+++ b/main/reference/summarized_experiment.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Example SummarizedExperiment Data — summarized_experiment • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example SummarizedExperiment Data — summarized_experiment"><meta name="description" content="
 This example SummarizedExperiment::SummarizedExperiment can be used to create a
-HermesData object. It already contains the required columns in rowData and colData."><title>Example SummarizedExperiment Data — summarized_experiment • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example SummarizedExperiment Data — summarized_experiment"><meta property="og:description" content="
+HermesData object. It already contains the required columns in rowData and colData."><meta property="og:description" content="
 This example SummarizedExperiment::SummarizedExperiment can be used to create a
-HermesData object. It already contains the required columns in rowData and colData."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+HermesData object. It already contains the required columns in rowData and colData."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,61 +11,39 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/hermes.html">Get started</a>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
-<!-- end dropdown for versions -->
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
-    <span class="fa fa-github"></span>
-     
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Example <code>SummarizedExperiment</code> Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>summarized_experiment.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p><a href="https://lifecycle.r-lib.org/articles/stages.html#stable" class="external-link"><img src="figures/lifecycle-stable.svg" alt="[Stable]"></a></p>
-<p>This example <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> can be used to create a
+<p>This example <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> can be used to create a
 <code><a href="HermesData-class.html">HermesData</a></code> object. It already contains the required columns in <code>rowData</code> and <code>colData</code>.</p>
     </div>
 
@@ -79,7 +54,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a> object with 20 samples covering
+    <p>A <a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a> object with 20 samples covering
 5085 features (<code>Entrez</code> gene IDs).</p>
     </div>
     <div class="section level2">
@@ -91,7 +66,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     <div class="dont-index"><p><code><a href="expression_set.html">expression_set</a></code> which contains similar data as a <code><a href="https://rdrr.io/pkg/Biobase/man/class.ExpressionSet.html" class="external-link">Biobase::ExpressionSet</a></code>.</p></div>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -100,14 +75,14 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/summary,AnyHermesData-method.html b/main/reference/summary,AnyHermesData-method.html
new file mode 100644
index 00000000..95206edb
--- /dev/null
+++ b/main/reference/summary,AnyHermesData-method.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/summary.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/summary.html">
+  </head>
+</html>
+
diff --git a/main/reference/summary.html b/main/reference/summary.html
index 2002037a..640b632b 100644
--- a/main/reference/summary.html
+++ b/main/reference/summary.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
-Provides a concise summary of the content of AnyHermesData objects."><title>Summary Method for AnyHermesData Objects — summary • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summary Method for AnyHermesData Objects — summary"><meta property="og:description" content="
-Provides a concise summary of the content of AnyHermesData objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Summary Method for AnyHermesData Objects — summary • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Summary Method for AnyHermesData Objects — summary"><meta name="description" content="
+Provides a concise summary of the content of AnyHermesData objects."><meta property="og:description" content="
+Provides a concise summary of the content of AnyHermesData objects."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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@@ -12,55 +9,33 @@
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Summary Method for <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-methods.R" class="external-link"><code>R/HermesData-methods.R</code></a></small>
       <div class="d-none name"><code>summary.Rd</code></div>
     </div>
 
@@ -73,34 +48,34 @@
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summary</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for AnyHermesData</span></span>
+<span><span class="co"># S4 method for class 'AnyHermesData'</span></span>
 <span><span class="fu">summary</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for HermesDataSummary</span></span>
+<span><span class="co"># S4 method for class 'HermesDataSummary'</span></span>
 <span><span class="fu"><a href="show.html">show</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>HermesDataSummary</code>) <br> result from the summary method applied to
 <code><a href="HermesData-class.html">AnyHermesData</a></code> object.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>not used.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>An object of the corresponding summary class, here
+    <p>An object of the corresponding summary class, here
 <code>HermesDataSummary</code>.</p>
     </div>
     <div class="section level2">
     <h2 id="methods-by-class-">Methods (by class)<a class="anchor" aria-label="anchor" href="#methods-by-class-"></a></h2>
-    
+
 <ul><li><p><code>summary(AnyHermesData)</code>: A summary method for <code><a href="HermesData-class.html">AnyHermesData</a></code> object that
 creates a <code>HermesDataSummary</code> object.</p></li>
 <li><p><code>show(HermesDataSummary)</code>: A show method prints summary description of <code>HermesDataSummary</code> object
@@ -155,7 +130,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>   06520062C0017R</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -164,14 +139,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/test_proportion.html b/main/reference/test_proportion.html
new file mode 100644
index 00000000..fec621f4
--- /dev/null
+++ b/main/reference/test_proportion.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/check_proportion.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/check_proportion.html">
+  </head>
+</html>
+
diff --git a/main/reference/top_genes-1.png b/main/reference/top_genes-1.png
index 4a027aef..e70978cf 100644
Binary files a/main/reference/top_genes-1.png and b/main/reference/top_genes-1.png differ
diff --git a/main/reference/top_genes-2.png b/main/reference/top_genes-2.png
index 50358431..e38ee74a 100644
Binary files a/main/reference/top_genes-2.png and b/main/reference/top_genes-2.png differ
diff --git a/main/reference/top_genes.html b/main/reference/top_genes.html
index 00591045..3562fff2 100644
--- a/main/reference/top_genes.html
+++ b/main/reference/top_genes.html
@@ -1,22 +1,19 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Derivation of Top Genes — top_genes • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Derivation of Top Genes — top_genes"><meta name="description" content="
 top_genes() creates a HermesDataTopGenes object, which extends data.frame. It
 contains two columns:
 expression: containing the statistic values calculated by summary_fun across columns.
 name: the gene names.
 
 
-The corresponding autoplot() method then visualizes the result as a barplot."><title>Derivation of Top Genes — top_genes • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Derivation of Top Genes — top_genes"><meta property="og:description" content="
+The corresponding autoplot() method then visualizes the result as a barplot."><meta property="og:description" content="
 top_genes() creates a HermesDataTopGenes object, which extends data.frame. It
 contains two columns:
 expression: containing the statistic values calculated by summary_fun across columns.
 name: the gene names.
 
 
-The corresponding autoplot() method then visualizes the result as a barplot."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+The corresponding autoplot() method then visualizes the result as a barplot."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -24,55 +21,33 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-      <ul class="navbar-nav me-auto"><li class="nav-item">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/hermes/v1.7.1">v1.7.1</a> </div></li>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Derivation of Top Genes</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/top_genes.R" class="external-link"><code>R/top_genes.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/top_genes.R" class="external-link"><code>R/top_genes.R</code></a></small>
       <div class="d-none name"><code>top_genes.Rd</code></div>
     </div>
 
@@ -94,7 +69,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  min_threshold <span class="op">=</span> <span class="cn">NULL</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="co"># S4 method for HermesDataTopGenes</span></span>
+<span><span class="co"># S4 method for class 'HermesDataTopGenes'</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span></span>
 <span>  <span class="va">object</span>,</span>
 <span>  x_lab <span class="op">=</span> <span class="st">"HGNC gene names"</span>,</span>
@@ -105,49 +80,49 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>AnyHermedData</code>)<br> input.</p></dd>
 
 
-<dt>assay_name</dt>
+<dt id="arg-assay-name">assay_name<a class="anchor" aria-label="anchor" href="#arg-assay-name"></a></dt>
 <dd><p>(<code>string</code>)<br> name of the assay to use for the sorting of genes.</p></dd>
 
 
-<dt>summary_fun</dt>
+<dt id="arg-summary-fun">summary_fun<a class="anchor" aria-label="anchor" href="#arg-summary-fun"></a></dt>
 <dd><p>(<code>function</code>)<br> summary statistics function to apply across the samples in
 the assay resulting in a numeric vector with one value per gene.</p></dd>
 
 
-<dt>n_top</dt>
+<dt id="arg-n-top">n_top<a class="anchor" aria-label="anchor" href="#arg-n-top"></a></dt>
 <dd><p>(<code>count</code> or <code>NULL</code>)<br> selection criteria based on number of entries.</p></dd>
 
 
-<dt>min_threshold</dt>
+<dt id="arg-min-threshold">min_threshold<a class="anchor" aria-label="anchor" href="#arg-min-threshold"></a></dt>
 <dd><p>(<code>number</code> or <code>NULL</code> )<br> selection criteria based on a minimum
 summary statistics threshold.</p></dd>
 
 
-<dt>x_lab</dt>
+<dt id="arg-x-lab">x_lab<a class="anchor" aria-label="anchor" href="#arg-x-lab"></a></dt>
 <dd><p>(<code>string</code>)<br> x-axis label.</p></dd>
 
 
-<dt>y_lab</dt>
+<dt id="arg-y-lab">y_lab<a class="anchor" aria-label="anchor" href="#arg-y-lab"></a></dt>
 <dd><p>(<code>string</code>)<br> y-axis label.</p></dd>
 
 
-<dt>title</dt>
+<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
 <dd><p>(<code>string</code>)<br> plot title.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A HermesDataTopGenes object.</p>
+    <p>A HermesDataTopGenes object.</p>
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    
+
 <ul><li><p>The data frame is sorted in descending order of <code>expression</code> and only the top
 entries according to the selection criteria are included.</p></li>
 <li><p>Note that exactly one of the arguments <code>n_top</code> and <code>min_threshold</code> must be
@@ -155,7 +130,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 </ul></div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>autoplot(HermesDataTopGenes)</code>: Creates a bar plot from a HermesDataTopGenes object,
 where the y axis shows the expression statistics for each of the top genes
 on the x-axis.</p></li>
@@ -201,7 +176,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-plt img"><img src="top_genes-2.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -210,14 +185,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/validate.html b/main/reference/validate.html
index 4ef33d52..6e85b026 100644
--- a/main/reference/validate.html
+++ b/main/reference/validate.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions are used internally only and therefore not exported. They work on
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Internal Helper Functions for Validation of AnyHermesData Objects — validate • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal Helper Functions for Validation of AnyHermesData Objects — validate"><meta name="description" content="These functions are used internally only and therefore not exported. They work on
 SummarizedExperiment::SummarizedExperiment objects, and AnyHermesData objects are
-defined by successfully passing these validation checks."><title>Internal Helper Functions for Validation of AnyHermesData Objects — validate • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal Helper Functions for Validation of AnyHermesData Objects — validate"><meta property="og:description" content="These functions are used internally only and therefore not exported. They work on
+defined by successfully passing these validation checks."><meta property="og:description" content="These functions are used internally only and therefore not exported. They work on
 SummarizedExperiment::SummarizedExperiment objects, and AnyHermesData objects are
-defined by successfully passing these validation checks."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+defined by successfully passing these validation checks."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,61 +11,39 @@
   gtag('config', 'UA-125641273-1');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://github.com/insightsengineering/hermes">
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/hermes"><span class="fa fa-github"></span></a></li>
       </ul></div>
 
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Internal Helper Functions for Validation of <code>AnyHermesData</code> Objects</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/HermesData-validate.R" class="external-link"><code>R/HermesData-validate.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/HermesData-validate.R" class="external-link"><code>R/HermesData-validate.R</code></a></small>
       <div class="d-none name"><code>validate.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>These functions are used internally only and therefore not exported. They work on
-<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> objects, and <code><a href="HermesData-class.html">AnyHermesData</a></code> objects are
+<code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> objects, and <code><a href="HermesData-class.html">AnyHermesData</a></code> objects are
 defined by successfully passing these validation checks.</p>
     </div>
 
@@ -89,28 +64,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>object</dt>
+
+
+<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
 <dd><p>(<code>SummarizedExperiment</code>)<br> object to validate.</p></dd>
 
 
-<dt>required</dt>
+<dt id="arg-required">required<a class="anchor" aria-label="anchor" href="#arg-required"></a></dt>
 <dd><p>(<code>character</code>)<br> required column names.</p></dd>
 
 
-<dt>actual</dt>
+<dt id="arg-actual">actual<a class="anchor" aria-label="anchor" href="#arg-actual"></a></dt>
 <dd><p>(<code>actual</code>)<br> actual column names.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A character vector with the validation failure messages, or <code>NULL</code> in
+    <p>A character vector with the validation failure messages, or <code>NULL</code> in
 case validation passes.</p>
     </div>
     <div class="section level2">
     <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2>
-    
+
 <ul><li><p><code>validate_counts()</code>: validates that the first assay is <code>counts</code> containing
 non-missing, integer, non-negative values.</p></li>
 <li><p><code>validate_cols()</code>: validates that required column names are contained in
@@ -124,7 +99,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 and only contains alphabetic characters.</p></li>
 </ul></div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -133,14 +108,14 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/main/reference/validate_col_data.html b/main/reference/validate_col_data.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_col_data.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/validate.html">
+  </head>
+</html>
+
diff --git a/main/reference/validate_cols.html b/main/reference/validate_cols.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_cols.html
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+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
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+  </head>
+</html>
+
diff --git a/main/reference/validate_counts.html b/main/reference/validate_counts.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_counts.html
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+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
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+  </head>
+</html>
+
diff --git a/main/reference/validate_names.html b/main/reference/validate_names.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_names.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/validate.html">
+  </head>
+</html>
+
diff --git a/main/reference/validate_prefix.html b/main/reference/validate_prefix.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_prefix.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/validate.html">
+  </head>
+</html>
+
diff --git a/main/reference/validate_row_data.html b/main/reference/validate_row_data.html
new file mode 100644
index 00000000..572ac635
--- /dev/null
+++ b/main/reference/validate_row_data.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://insightsengineering.github.io/hermes/reference/validate.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://insightsengineering.github.io/hermes/reference/validate.html">
+  </head>
+</html>
+
diff --git a/main/reference/wrap_in_mae.html b/main/reference/wrap_in_mae.html
index 25fe91ec..540e635d 100644
--- a/main/reference/wrap_in_mae.html
+++ b/main/reference/wrap_in_mae.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Wrap in MAE — wrap_in_mae • hermes</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Wrap in MAE — wrap_in_mae"><meta name="description" content="
 This helper function wraps SummarizedExperiment objects into an
-a MultiAssayExperiment (MAE) object."><title>Wrap in MAE — wrap_in_mae • hermes</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Wrap in MAE — wrap_in_mae"><meta property="og:description" content="
+a MultiAssayExperiment (MAE) object."><meta property="og:description" content="
 This helper function wraps SummarizedExperiment objects into an
-a MultiAssayExperiment (MAE) object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
+a MultiAssayExperiment (MAE) object."><meta property="og:image" content="https://insightsengineering.github.io/hermes/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=UA-125641273-1"></script><script>
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   gtag('js', new Date());
@@ -14,55 +11,33 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.7.2.9003</small>
+
 
-    
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../articles/hermes.html">Get started</a></li>
+<li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Wrap in MAE</h1>
-      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/HEAD/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/insightsengineering/hermes/blob/main/R/utils.R" class="external-link"><code>R/utils.R</code></a></small>
       <div class="d-none name"><code>wrap_in_mae.Rd</code></div>
     </div>
 
@@ -79,19 +54,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>(<code>SummarizedExperiment</code>)<br> input to create the MAE object from.</p></dd>
 
 
-<dt>name</dt>
+<dt id="arg-name">name<a class="anchor" aria-label="anchor" href="#arg-name"></a></dt>
 <dd><p>(<code>string</code>)<br> experiment name to use in the MAE for <code>x</code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>The MAE object with the only experiment being <code>x</code> having the given
+    <p>The MAE object with the only experiment being <code>x</code> having the given
 <code>name</code>.</p>
     </div>
 
@@ -112,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>   TechnicalFailureFlag</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -121,14 +96,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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diff --git a/main/search.json b/main/search.json
index fd1e40b7..ea90c790 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"acknowledgments","dir":"Articles","previous_headings":"","what":"Acknowledgments","title":"Introduction to `hermes`","text":"hermes successor Roche internal rnaseqTools R package, therefore many code ideas borrowed . Therefore like thank rnaseqTools authors work. particular, like acknowledge Chendi Liao Joe Paulson guidance explanations development hermes. also discussed class design Valerie Obenchain, discussed RNAseq data standards Armen Karapetyan. borrowed ideas Roche internal biokitr R package discussed maintainer Daniel Marbach. Finally, hermes originated part NEST project. grateful entire team’s support. Thanks lot everyone involved!","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to `hermes`","text":"First let’s see can install hermes package.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"bioconductor","dir":"Articles","previous_headings":"Installation","what":"BioConductor","title":"Introduction to `hermes`","text":"development version (3.15) BioConductor, can install current package version :","code":"if (!require(\"BiocManager\")) {   install.packages(\"BiocManager\") } BiocManager::install(\"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"github","dir":"Articles","previous_headings":"Installation","what":"GitHub","title":"Introduction to `hermes`","text":"can install unstable development version GitHub :","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } devtools::install_github(\"insightsengineering/hermes\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction to `hermes`","text":"hermes R package provides classes, methods functions import, quality-check, filter, normalize, analyze RNAseq counts data. core functionality built BioConductor ecosystem, especially SummarizedExperiment. vignette read new users package. vignette going learn : Import RNAseq count data hermes ready format. Annotate gene information automatically central database (e.g. BioMart). Add quality control (QC) flags genes samples. Filter data set. Normalize counts. Quickly produce descriptive plots. Perform principal components analysis. Produce templated QC report. Perform differential expression analysis. packages used vignette : datasets used vignette :","code":"library(hermes) library(SummarizedExperiment) ?expression_set ?summarized_experiment"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"importing-data","dir":"Articles","previous_headings":"","what":"Importing Data","title":"Introduction to `hermes`","text":"data hermes needs imported HermesData RangedHermesData format.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"importing-a-summarizedexperiment","dir":"Articles","previous_headings":"Importing Data","what":"Importing a SummarizedExperiment","title":"Introduction to `hermes`","text":"simplest way import data SummarizedExperiment (SE) object. HermesData object just special SE, additional requirements slots. nutshell, object needs counts assay, certain gene sample variables, unique row column names. row names, .e. gene names, must start common prefix GeneID ENSG enable easy annotations. See ?HermesData detailed requirements. SE follows minimum conventions, can just call HermesData constructor : HermesData object. Note case deprecated names used rowData colData variables, therefore appear “additional” gene sample information. However can still call default constructor new names filled missing values, e.g.: want map old column names new column names avoid duplication new missing value columns, can using rename() method. example : example can now see annotations successfully carried information since mapped old annotations new required names : bit details can also call summary() object. , let’s use already prepared HermesData object. Likewise, receive error “‘counts’ assay found”, can use rename() function change name assay SummarizedExperiment object counts. example, following object type SummarizedExperiment assay name count, produce assay name error: use following code convert assay name counts, making able convert HermesData object:","code":"object <- HermesData(summarized_experiment) object #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                     symbol      desc chromosome      size #>                  <logical> <logical>  <logical> <logical> #> GeneID:11185            NA        NA         NA        NA #> GeneID:10677            NA        NA         NA        NA #> GeneID:101928428        NA        NA         NA        NA #> GeneID:100422835        NA        NA         NA        NA #> GeneID:102466731        NA        NA         NA        NA #> GeneID:64881            NA        NA         NA        NA object <- summarized_experiment %>%   rename(     row_data = c(       symbol = \"HGNC\",       desc = \"HGNCGeneName\",       chromosome = \"Chromosome\",       size = \"WidthBP\",       low_expression_flag = \"LowExpressionFlag\"     ),     col_data = c(       low_depth_flag = \"LowDepthFlag\",       technical_failure_flag = \"TechnicalFailureFlag\"     )   ) %>%   HermesData() head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                        symbol                   desc  chromosome      size #>                   <character>            <character> <character> <integer> #> GeneID:11185             INMT indolethylamine N-me..           7      5468 #> GeneID:10677             AVIL               advillin          12     18694 #> GeneID:101928428 LOC101928428 RNA-binding protein ..  GL000220.1       138 #> GeneID:100422835      MIR3183          microRNA 3183          17        84 #> GeneID:102466731     MIR6769A         microRNA 6769a          16        73 #> GeneID:64881           PCDH20       protocadherin 20          13      5838 summary(object) #> HermesData object with 20 samples of 5085 genes. #> - Library sizes across samples: mean 5476759, median 5365970, range 4632496 to 7262374 #> - Included assays (1): counts #> - Additional gene information (7): GeneID StartBP ... SYMBOL #>   chromosome_name #> - Additional sample information (73): Filename SampleID ... STDSSDY #>   technical_failure_flag #> - Low expression genes (3021): GeneID:10677 GeneID:101928428 ... #>   GeneID:9084 GeneID:9426 #> - Samples with too low depth or technical failures (20): NA NA ... NA #>   NA object <- hermes_data object_exp <- summarized_experiment %>%   rename(assays = c(count = \"counts\")) object_exp <- rename(object_exp,   assays = c(counts = \"count\") ) object_exp <- HermesData(object_exp)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"importing-an-expressionset","dir":"Articles","previous_headings":"Importing Data","what":"Importing an ExpressionSet","title":"Introduction to `hermes`","text":"start ExpressionSet, can first convert RangedSummarizedExperiment import RangedHermesData:","code":"se <- makeSummarizedExperimentFromExpressionSet(expression_set) object2 <- HermesData(se) object2 #> class: RangedHermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"importing-a-matrix","dir":"Articles","previous_headings":"Importing Data","what":"Importing a Matrix","title":"Introduction to `hermes`","text":"general can also import matrix counts. just pass required gene sample information data frames constructor. Note can easily access counts assay (matrix) final object counts():","code":"counts_matrix <- assay(hermes_data) object3 <- HermesDataFromMatrix(   counts = counts_matrix,   rowData = rowData(hermes_data),   colData = colData(hermes_data) ) object3 #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY identical(object, object3) #> [1] TRUE cnts <- counts(object) cnts[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185                  3             66             35 #> GeneID:10677               1668            236             95 #> GeneID:101928428              0              0              0"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"annotations","dir":"Articles","previous_headings":"","what":"Annotations","title":"Introduction to `hermes`","text":"hermes provides modular approach querying gene annotations, order allow future extensions downstream packages.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"connection-to-database","dir":"Articles","previous_headings":"Annotations","what":"Connection to Database","title":"Introduction to `hermes`","text":"first step connect database. hermes option currently databases utilize BioMart software suite. However due generic function design, simple extend hermes data base connections. order save time vignette build, zoom subset original object containing first 10 genes. corresponding function takes common gene ID prefix argument determine format gene IDs filter variable use query later . using prefix() method access prefix saved HermesData object.","code":"small_object <- object[1:10, ] httr::set_config(httr::config(ssl_verifypeer = 0L)) connection <- connect_biomart(prefix(small_object))"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"querying-and-saving-annotations","dir":"Articles","previous_headings":"Annotations","what":"Querying and Saving Annotations","title":"Introduction to `hermes`","text":"second step query gene annotations save object. using genes() method access gene IDs (row names) HermesData object. Note genes might found data base corresponding rows NA annotations.","code":"annotation(small_object) <- query(genes(small_object), connection)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"quality-control-flags","dir":"Articles","previous_headings":"","what":"Quality Control Flags","title":"Introduction to `hermes`","text":"hermes provides automatic gene sample flagging, well manual sample flagging functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"automatic-gene-and-sample-flagging","dir":"Articles","previous_headings":"Quality Control Flags","what":"Automatic Gene and Sample Flagging","title":"Introduction to `hermes`","text":"genes, counted many samples don’t pass minimum expression CPM (counts per million reads mapped) threshold. many, gene flagged “low expression” gene. samples, two flags provided. “technical failure” flag based average Pearson correlation samples. “low depth” flag based library size, .e. total sum counts sample across genes. Thresholds flags can initialized control_quality(), flags added add_quality_flags().","code":"my_controls <- control_quality(min_cpm = 10, min_cpm_prop = 0.4, min_corr = 0.4, min_depth = 1e4) #> Loading required namespace: testthat object_flagged <- add_quality_flags(object, control = my_controls)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"manual-sample-flagging","dir":"Articles","previous_headings":"Quality Control Flags","what":"Manual Sample Flagging","title":"Introduction to `hermes`","text":"Sometimes necessary manually flag certain samples technical failures, e.g. looking one analyses discussed . possible, .","code":"object_flagged <- set_tech_failure(object_flagged, sample_ids = \"06520011B0023R\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"accessing-flags","dir":"Articles","previous_headings":"Quality Control Flags","what":"Accessing Flags","title":"Introduction to `hermes`","text":"flags access functions.","code":"head(get_tech_failure(object_flagged)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>           TRUE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE head(get_low_depth(object_flagged)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE head(get_low_expression(object_flagged)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>             TRUE            FALSE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"filtering-data","dir":"Articles","previous_headings":"","what":"Filtering Data","title":"Introduction to `hermes`","text":"can either filter based default QC flags, based custom variables gene sample information.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"based-on-default-qc-flags","dir":"Articles","previous_headings":"Filtering Data","what":"Based on Default QC Flags","title":"Introduction to `hermes`","text":"simple filter() function. also possible selectively filter genes samples using argument.","code":"object_flagged_filtered <- filter(object_flagged) object_flagged_genes_filtered <- filter(object_flagged, what = \"genes\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"based-on-custom-variables","dir":"Articles","previous_headings":"Filtering Data","what":"Based on Custom Variables","title":"Introduction to `hermes`","text":"can done subset() function. Genes can filtered subset argument via expressions using gene information variables, samples can filtered select argument using sample information variables. order see ones available can queries first.","code":"names(rowData(object_flagged)) #> [1] \"symbol\"              \"desc\"                \"GeneID\"              #> [4] \"chromosome\"          \"size\"                \"SYMBOL\"              #> [7] \"chromosome_name\"     \"low_expression_flag\" names(colData(object_flagged)) #>  [1] \"Filename\"          \"SampleID\"          \"AGEGRP\"            #>  [4] \"AGE18\"             \"STDDRS\"            \"STDDRSD\"           #>  [7] \"STDSSDT\"           \"TRTDRS\"            \"TRTDRSD\"           #> [10] \"BHDCIRC\"           \"BHDCIRCU\"          \"ADAFL\"             #> [13] \"BLANP\"             \"BKPS\"              \"BLKS\"              #> [16] \"BTANNER\"           \"FRPST\"             \"DURIDX\"            #> [19] \"DURSAF\"            \"DURSUR\"            \"LNTHRPY\"           #> [22] \"AENCIFL\"           \"STUDYID\"           \"USUBJID\"           #> [25] \"RFSTDTC\"           \"RFENDTC\"           \"RFXSTDTC\"          #> [28] \"RFXENDTC\"          \"RFICDTC\"           \"RFPENDTC\"          #> [31] \"DTHDTC\"            \"DTHFL\"             \"SITEID\"            #> [34] \"INVID\"             \"AGE\"               \"AGEU\"              #> [37] \"SEX\"               \"RACE\"              \"ETHNIC\"            #> [40] \"ARMCD\"             \"ARM\"               \"ACTARMCD\"          #> [43] \"ACTARM\"            \"COUNTRY\"           \"DMDTC\"             #> [46] \"DMDY\"              \"BAGE\"              \"BAGEU\"             #> [49] \"BWT\"               \"BWTU\"              \"BHT\"               #> [52] \"BHTU\"              \"BBMI\"              \"ITTFL\"             #> [55] \"SAFFL\"             \"INFCODT\"           \"RANDDT\"            #> [58] \"TRTSDTC\"           \"TRTSDTM\"           \"TRTSTMF\"           #> [61] \"TRTEDTM\"           \"TRTETMF\"           \"TRTDUR\"            #> [64] \"DISCSTUD\"          \"DISCDEAT\"          \"DISCAE\"            #> [67] \"DISTRTFL\"          \"AEWITHFL\"          \"ALIVDT\"            #> [70] \"COHORT\"            \"TTYPE\"             \"STDSSDY\"           #> [73] \"low_depth_flag\"    \"tech_failure_flag\" head(rowData(object_flagged)$chromosome) #> [1] \"7\"          \"12\"         \"GL000220.1\" \"17\"         \"16\"         #> [6] \"13\" head(object_flagged$ARMCD) #> [1] \"COH1\"  \"COH1\"  \"COH8\"  \"COH12\" \"COH9O\" \"COH9E\" object_flagged_subsetted <- subset(   object_flagged,   subset = chromosome == \"5\",   select = ARMCD == \"COH1\" )"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"normalizing-counts","dir":"Articles","previous_headings":"","what":"Normalizing Counts","title":"Introduction to `hermes`","text":"Normalizing counts within samples (CPM), genes (RPKM) across (TPM) can achieved normalize() function. normalize() function can also transform counts variance stabilizing transformation (vst) regularized log transformation (rlog) proposed DESeq2 package. corresponding assays saved object can accessed assay(). used control settings can accessed afterwards metadata object: Note also filtering settings saved . custom normalization options, use control_normalize(). example, use log scale original scale counts:","code":"object_normalized <- normalize(object_flagged_filtered) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. object_rlog_normalized <- normalize(object_flagged_filtered, \"rlog\") #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. assay(object_normalized, \"tpm\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677        4.096418       3.323016       7.714990 #> GeneID:286205       2.985506       3.182624       3.769962 #> GeneID:8365        11.711741      12.421108      12.466491 assay(object_rlog_normalized, \"rlog\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677        8.101651       7.153488      10.281393 #> GeneID:286205      10.101287       9.859074      10.104426 #> GeneID:8365        10.023097      10.163191       9.935722 metadata(object_normalized) #> $control_quality_flags #> $control_quality_flags$min_cpm #> [1] 10 #>  #> $control_quality_flags$min_cpm_prop #> [1] 0.4 #>  #> $control_quality_flags$min_corr #> [1] 0.4 #>  #> $control_quality_flags$min_depth #> [1] 10000 #>  #>  #> $control_normalize #> $control_normalize$log #> [1] TRUE #>  #> $control_normalize$lib_sizes #> NULL #>  #> $control_normalize$prior_count #> [1] 1 #>  #> $control_normalize$fit_type #> [1] \"parametric\" object_normalized_original <- normalize(   object_flagged_filtered,   control = control_normalize(log = FALSE) ) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. assay(object_normalized_original, \"tpm\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677       16.105854       9.007544       209.1084 #> GeneID:286205       6.920033       8.079569        12.6418 #> GeneID:8365      3353.172671    5483.360511      5658.6256"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"simple-plots","dir":"Articles","previous_headings":"Descriptive Plots","what":"Simple Plots","title":"Introduction to `hermes`","text":"series simple descriptive plots can obtained just calling autoplot() object.  Note individual plots can produced series draw_*() functions, see ?plot_all detailed list. , can customized . example, can change number color bins library size histogram:","code":"autoplot(object) draw_libsize_hist(object, bins = 10L, fill = \"blue\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"top-genes","dir":"Articles","previous_headings":"Descriptive Plots","what":"Top Genes","title":"Introduction to `hermes`","text":"Top genes can calculated visualized barplot.  passing another summary function, also variability can ranked example.","code":"most_expr_genes <- top_genes(object_normalized, assay_name = \"tpm\") autoplot(most_expr_genes) most_var_genes <- top_genes(object_normalized, summary_fun = rowSds) autoplot(most_var_genes)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"heatmap-of-genes-among-samples","dir":"Articles","previous_headings":"Descriptive Plots","what":"Heatmap of Genes among Samples","title":"Introduction to `hermes`","text":"Relative expression genes can displayed using heatmap  heatmap can grouped labels HermesData object, \"COUNTRY\" \"AGEGRP\".","code":"draw_heatmap(object[1:20], assay_name = \"counts\") draw_heatmap(object[1:20], assay_name = \"counts\", col_data_annotation = \"COUNTRY\")"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"correlation-between-samples","dir":"Articles","previous_headings":"Descriptive Plots","what":"Correlation between Samples","title":"Introduction to `hermes`","text":"sample correlation matrix samples can obtained correlate() function. can visualized heatmap using autoplot() . See ?calc_cor detailed options.","code":"cor_mat <- correlate(object) autoplot(cor_mat)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"principal-components","dir":"Articles","previous_headings":"","what":"Principal Components","title":"Introduction to `hermes`","text":"Let’s see can perform Principal Components Analysis (PCA).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"pca-of-samples","dir":"Articles","previous_headings":"Principal Components","what":"PCA of Samples","title":"Introduction to `hermes`","text":"PCA can performed calc_pca(). result can summarized plotted.  Note various options available plot, example can look different principal components, color samples sample variables. See ?ggfortify::autoplot.prcomp details.","code":"pca_res <- calc_pca(object_normalized, assay_name = \"tpm\") summary(pca_res)$importance #>                             PC1      PC2      PC3      PC4      PC5      PC6 #> Standard deviation     22.08095 17.34762 15.19930 12.80689 11.76153 10.48121 #> Proportion of Variance  0.24066  0.14854  0.11403  0.08096  0.06828  0.05422 #> Cumulative Proportion   0.24066  0.38919  0.50322  0.58418  0.65246  0.70668 #>                             PC7      PC8      PC9     PC10     PC11     PC12 #> Standard deviation     9.812505 8.950926 8.530826 8.196006 7.905973 7.216002 #> Proportion of Variance 0.047520 0.039550 0.035920 0.033160 0.030850 0.025700 #> Cumulative Proportion  0.754200 0.793750 0.829670 0.862830 0.893680 0.919380 #>                           PC13     PC14     PC15     PC16     PC17              #> Standard deviation     6.92755 6.532485 5.501383 5.151959 3.983283 2.272579e-14 #> Proportion of Variance 0.02369 0.021060 0.014940 0.013100 0.007830 0.000000e+00 #> Cumulative Proportion  0.94307 0.964130 0.979070 0.992170 1.000000 1.000000e+00 autoplot(pca_res) autoplot(   pca_res,   x = 2, y = 3,   data = as.data.frame(colData(object_normalized)), colour = \"SEX\" )"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"correlation-with-sample-variables","dir":"Articles","previous_headings":"Principal Components","what":"Correlation with Sample Variables","title":"Introduction to `hermes`","text":"Subsequently easy correlate obtained principal components sample variables. obtain matrix R-squared (R2) values combinations, can visualized heatmap. See ?pca_cor_samplevar details.","code":"pca_cor <- correlate(pca_res, object_normalized) autoplot(pca_cor)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"qc-report-template","dir":"Articles","previous_headings":"","what":"QC Report Template","title":"Introduction to `hermes`","text":"order quickly obtain quality control report new RNAseq data set, can proceed follows. Save input SummarizedExperiment using R’s save() function binary data file (e.g. ending .rda suffix). Load hermes package RStudio click : File > New File > R Markdown > Template select QC report template hermes. Fill parameters yaml header, including required file paths input file , resulting HermesData object saved. Knit document. report contains mentioned descriptive plots PCA analyses can useful starting point analysis.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"differential-expression","dir":"Articles","previous_headings":"","what":"Differential Expression","title":"Introduction to `hermes`","text":"addition QC analyses, simple differential expression analysis supported hermes. addition filtered object (normalization counts required) variable name factor contrast samples needs provided diff_expression(). Note use utility function df_cols_to_factor() converts default character logical variables factor variables. one possible way ensure utilized group variable factor. Afterwards standard volcano plot can produced.","code":"colData(object) <- df_cols_to_factor(colData(object)) diff_res <- diff_expression(object, group = \"SEX\", method = \"voom\") head(diff_res) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -4.239244 0.0004209192 0.9118348 #> GeneID:51227  -1.0467295 -4.032550 0.0006788432 0.9118348 #> GeneID:344558  1.6896266  3.824046 0.0010993677 0.9118348 #> GeneID:51575  -0.7760844 -3.746293 0.0013155805 0.9118348 #> GeneID:151242 -3.4358998 -3.570103 0.0019741997 0.9118348 #> GeneID:8904   -0.6100354 -3.542864 0.0021017199 0.9118348 autoplot(diff_res, log2_fc_thresh = 8)"},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to `hermes`","text":"hermes R package provides classes, methods functions import, quality-check, filter, normalize analyze RNAseq counts data. particular, robust object-oriented framework allows easy extensions future address user feature requests. feedback welcome - thank much advance thoughts hermes!","code":""},{"path":"https://insightsengineering.github.io/hermes/main/articles/hermes.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Introduction to `hermes`","text":"output sessionInfo() system document compiled running pandoc 3.2:","code":"#> R version 4.4.0 (2024-04-24) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] hermes_1.7.2.9000           SummarizedExperiment_1.34.0 #>  [3] Biobase_2.64.0              GenomicRanges_1.56.1        #>  [5] GenomeInfoDb_1.40.1         IRanges_2.38.0              #>  [7] S4Vectors_0.42.0            BiocGenerics_0.50.0         #>  [9] MatrixGenerics_1.16.0       matrixStats_1.3.0           #> [11] ggfortify_0.4.17            ggplot2_3.5.1               #> [13] BiocStyle_2.32.1            #>  #> loaded via a namespace (and not attached): #>   [1] Rdpack_2.6                  DBI_1.2.3                   #>   [3] httr2_1.0.1                 gridExtra_2.3               #>   [5] testthat_3.2.1.1            biomaRt_2.60.1              #>   [7] rlang_1.1.4                 magrittr_2.0.3              #>   [9] clue_0.3-65                 GetoptLong_1.0.5            #>  [11] compiler_4.4.0              RSQLite_2.3.7               #>  [13] png_0.1-8                   systemfonts_1.1.0           #>  [15] vctrs_0.6.5                 stringr_1.5.1               #>  [17] pkgconfig_2.0.3             shape_1.4.6.1               #>  [19] crayon_1.5.3                fastmap_1.2.0               #>  [21] magick_2.8.3                dbplyr_2.5.0                #>  [23] backports_1.5.0             XVector_0.44.0              #>  [25] labeling_0.4.3              utf8_1.2.4                  #>  [27] rmarkdown_2.27              UCSC.utils_1.0.0            #>  [29] ragg_1.3.2                  purrr_1.0.2                 #>  [31] bit_4.0.5                   xfun_0.45                   #>  [33] MultiAssayExperiment_1.30.2 zlibbioc_1.50.0             #>  [35] cachem_1.1.0                jsonlite_1.8.8              #>  [37] progress_1.2.3              EnvStats_2.8.1              #>  [39] blob_1.2.4                  highr_0.11                  #>  [41] DelayedArray_0.30.1         BiocParallel_1.38.0         #>  [43] prettyunits_1.2.0           parallel_4.4.0              #>  [45] cluster_2.1.6               R6_2.5.1                    #>  [47] bslib_0.7.0                 stringi_1.8.4               #>  [49] RColorBrewer_1.1-3          limma_3.60.3                #>  [51] brio_1.1.5                  jquerylib_0.1.4             #>  [53] Rcpp_1.0.12                 bookdown_0.40               #>  [55] assertthat_0.2.1            iterators_1.0.14            #>  [57] knitr_1.47                  Matrix_1.7-0                #>  [59] tidyselect_1.2.1            abind_1.4-5                 #>  [61] yaml_2.3.9                  doParallel_1.0.17           #>  [63] codetools_0.2-20            curl_5.2.1                  #>  [65] lattice_0.22-6              tibble_3.2.1                #>  [67] KEGGREST_1.44.1             withr_3.0.0                 #>  [69] evaluate_0.24.0             desc_1.4.3                  #>  [71] BiocFileCache_2.12.0        xml2_1.3.6                  #>  [73] Biostrings_2.72.1           circlize_0.4.16             #>  [75] filelock_1.0.3              pillar_1.9.0                #>  [77] BiocManager_1.30.23         checkmate_2.3.1             #>  [79] foreach_1.5.2               generics_0.1.3              #>  [81] hms_1.1.3                   munsell_0.5.1               #>  [83] scales_1.3.0                glue_1.7.0                  #>  [85] tools_4.4.0                 locfit_1.5-9.10             #>  [87] forcats_1.0.0               fs_1.6.4                    #>  [89] grid_4.4.0                  tidyr_1.3.1                 #>  [91] rbibutils_2.2.16            edgeR_4.2.0                 #>  [93] AnnotationDbi_1.66.0        colorspace_2.1-0            #>  [95] GenomeInfoDbData_1.2.12     cli_3.6.3                   #>  [97] rappdirs_0.3.3              textshaping_0.4.0           #>  [99] fansi_1.0.6                 S4Arrays_1.4.1              #> [101] ComplexHeatmap_2.20.0       dplyr_1.1.4                 #> [103] gtable_0.3.5                DESeq2_1.44.0               #> [105] sass_0.4.9                  digest_0.6.36               #> [107] SparseArray_1.4.8           ggrepel_0.9.5               #> [109] farver_2.1.2                rjson_0.2.21                #> [111] htmlwidgets_1.6.4           memoise_2.0.1               #> [113] htmltools_0.5.8.1           pkgdown_2.0.9               #> [115] lifecycle_1.0.4             httr_1.4.7                  #> [117] statmod_1.5.0               GlobalOptions_0.1.2         #> [119] bit64_4.0.5"},{"path":"https://insightsengineering.github.io/hermes/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Namrata Bhatia. Author. Stefanie Bienert. Author. Benoit Falquet. Author. Haocheng Li. Author. Jeff Luong. Author. Lyndsee Midori Zhang. Author. Alex Richardson. Author. Simona Rossomanno. Author. Tim Treis. Author. Mark Yan. Author. Naomi Chang. Author. Chendi Liao. Author. Carolyn Zhang. Author. Joseph N. Paulson. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Bhatia N, Bienert S, Falquet B, Li H, Luong J, Midori Zhang L, Richardson , Rossomanno S, Treis T, Yan M, Chang N, Liao C, Carolyn Zhang, Paulson J (2024). hermes: Preprocessing, analyzing, reporting RNA-seq data. R package version 1.7.2.9000, https://insightsengineering.github.io/hermes/main/.","code":"@Manual{,   title = {hermes: Preprocessing, analyzing, and reporting of RNA-seq data},   author = {Daniel {Sabanés Bové} and Namrata Bhatia and Stefanie Bienert and Benoit Falquet and Haocheng Li and Jeff Luong and Lyndsee {Midori Zhang} and Alex Richardson and Simona Rossomanno and Tim Treis and Mark Yan and Naomi Chang and Chendi Liao and {Carolyn Zhang} and Joseph N. Paulson},   year = {2024},   note = {R package version 1.7.2.9000},   url = {https://insightsengineering.github.io/hermes/main/}, }"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/index.html","id":"bioconductor","dir":"","previous_headings":"Installation","what":"BioConductor","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can install current release BioConductor :","code":"if (!require(\"BiocManager\")) {   install.packages(\"BiocManager\") } BiocManager::install(\"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/main/index.html","id":"github","dir":"","previous_headings":"Installation","what":"GitHub","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can install development version GitHub :","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } devtools::install_github(\"insightsengineering/hermes\")"},{"path":"https://insightsengineering.github.io/hermes/main/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can get started reading introduction vignette:","code":"library(hermes) vignette(\"introduction\", package = \"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"GeneSpec consists gene IDs (possibly named labels), summary function name summary function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"GeneSpec$new() GeneSpec$get_genes() GeneSpec$get_gene_labels() GeneSpec$returns_vector() GeneSpec$get_label() GeneSpec$extract() GeneSpec$extract_data_frame() GeneSpec$clone()","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Creates new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$new(genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (named character NULL) gene IDs, names used labels available. fun (function NULL) summary function. NULL used multiple genes summarized returned matrix extract method. fun_name (string) name summary function.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-get-genes-","dir":"Reference","previous_headings":"","what":"Method get_genes()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_genes()"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-get-gene-labels-","dir":"Reference","previous_headings":"","what":"Method get_gene_labels()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns gene labels (substituted gene IDs available).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_gene_labels(genes = self$get_genes())"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (character) subset genes labels returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-returns-vector-","dir":"Reference","previous_headings":"","what":"Method returns_vector()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Predicate whether extract returns vector .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$returns_vector()"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-get-label-","dir":"Reference","previous_headings":"","what":"Method get_label()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns string can used e.g. plot labels.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_label(genes = self$get_genes())"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (character) subset genes labels returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-extract-","dir":"Reference","previous_headings":"","what":"Method extract()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Extract gene values assay specified.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$extract(assay)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"assay (matrix) original matrix rownames containing specified genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Either vector one value per column, matrix multiple genes rows.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-extract-data-frame-","dir":"Reference","previous_headings":"","what":"Method extract_data_frame()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Extract gene values data.frame.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$extract_data_frame(assay)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"assay (matrix) original matrix rownames containing specified genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"data.frame genes columns samples rows.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/GeneSpec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"# Minimal specification if only one gene is used. x_spec <- gene_spec(\"GeneID:1820\")  # Using multiple genes with a signature. x_spec <- gene_spec(c(\"GeneID:1820\", \"GeneID:52\"), fun = colMeans) x_spec <- gene_spec(c(\"GeneID:1820\", \"GeneID:52\"), fun = colPrinComp1) x_spec$returns_vector() #> [1] TRUE x_spec$get_genes() #> [1] \"GeneID:1820\" \"GeneID:52\"   x_spec$get_gene_labels() #> [1] \"GeneID:1820\" \"GeneID:52\"   x_spec$get_label() #> [1] \"colPrinComp1(GeneID:1820, GeneID:52)\"  # Using multiple genes with partial labels, without a signature. x_spec <- gene_spec(c(A = \"GeneID:1820\", \"GeneID:52\")) x_spec$returns_vector() #> [1] FALSE x_spec$get_gene_labels() #> [1] \"A\"         \"GeneID:52\"  # Use the gene specification to extract genes from a matrix. mat <- matrix(   data = rpois(15, 10),   nrow = 3, ncol = 5,   dimnames = list(c(\"GeneID:1820\", \"GeneID:52\", \"GeneID:523\"), NULL) ) x_spec$extract(mat) #>           [,1] [,2] [,3] [,4] [,5] #> A            5   11    7   11   11 #> GeneID:52    6   13    9   16    7  # We can also extract these as a `data.frame`. x_spec$extract_data_frame(mat) #>    A GeneID.52 #> 1  5         6 #> 2 11        13 #> 3  7         9 #> 4 11        16 #> 5 11         7"},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"HermesData and RangedHermesData — HermesData-class","title":"HermesData and RangedHermesData — HermesData-class","text":"HermesData class extension SummarizedExperiment::SummarizedExperiment additional validation criteria.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HermesData and RangedHermesData — HermesData-class","text":"","code":"HermesData(object)  HermesDataFromMatrix(counts, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HermesData and RangedHermesData — HermesData-class","text":"object (SummarizedExperiment) input create HermesData object . RangedSummarizedExperiment, result RangedHermesData. counts (matrix) counts create HermesData object . ... additional arguments, e.g. rowData, colData, etc. passed SummarizedExperiment::SummarizedExperiment() internally. Note rowRanges passed instead rowData, result RangedHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"HermesData and RangedHermesData — HermesData-class","text":"object class AnyHermesData (HermesData RangedHermesData).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HermesData and RangedHermesData — HermesData-class","text":"additional criteria : first assay must counts containing non-missing, integer, non-negative values. Note rename() can used edit assay name counts needed. following columns must rowData: symbol (also often called HGNC similar, example: \"INMT\") desc (gene name, example: \"indolethylamine N-methyltransferase\") chromosome (chromosome string, example: \"7\") size (size gene base pairs, e.g 5468) low_expression_flag (can populated add_quality_flags()) following columns must colData: low_depth_flag (can populated add_quality_flags()) tech_failure_flag (can populated add_quality_flags()) object must unique row column names. row names gene names column names sample names. Analogously, RangedHermesData extension SummarizedExperiment::RangedSummarizedExperiment additional validation requirements. Methods can defined classes time AnyHermesData signature. Biobase::ExpressionSet object can imported using SummarizedExperiment::makeSummarizedExperimentFromExpressionSet() function first convert SummarizedExperiment::SummarizedExperiment object converting HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"HermesData and RangedHermesData — HermesData-class","text":"prefix common prefix gene IDs (row names).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"HermesData and RangedHermesData — HermesData-class","text":"Note use S4Vectors::setValidity2() define validity method, allows us turn validity checks internal functions intermediate objects may valid within scope function. can helpful convert character logical variables factors colData() (HermesData creation). provide utility function df_cols_to_factor() simplify task, leave user allow full control details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/HermesData-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"HermesData and RangedHermesData — HermesData-class","text":"","code":"# Convert an `ExpressionSet` to a `RangedSummarizedExperiment`. ranged_summarized_experiment <- makeSummarizedExperimentFromExpressionSet(expression_set)  # Then convert to `RangedHermesData`. HermesData(ranged_summarized_experiment) #> class: RangedHermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag  # Create objects starting from a `SummarizedExperiment`. hermes_data <- HermesData(summarized_experiment) hermes_data #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag  # Create objects from a matrix. Note that additional arguments are not required but possible. counts_matrix <- assay(summarized_experiment) counts_hermes_data <- HermesDataFromMatrix(counts_matrix)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/all_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks Whether All Missing — all_na","title":"Checks Whether All Missing — all_na","text":"Internal function check whether whole vector NA.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/all_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks Whether All Missing — all_na","text":"","code":"all_na(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/all_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks Whether All Missing — all_na","text":"x (vector) vector check.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/all_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks Whether All Missing — all_na","text":"Corresponding flag.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotation Accessor and Setter — annotation,AnyHermesData-method","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"methods access set gene annotations stored AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData annotation(object, ...)  .row_data_annotation_cols  # S4 method for AnyHermesData,DataFrame annotation(object) <- value"},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"annotation column names available exported character vector .row_data_annotation_cols.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"object (AnyHermesData) object access annotations . ... used. value (DataFrame) annotations replaced .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"S4Vectors::DataFrame gene annotations: symbol desc chromosome size","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"trying replace required annotations completely missing values genes, warning given corresponding gene IDs saved attribute annotation.missing.genes. Note also additional annotations beyond required ones may supplied stored.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"","code":"object <- hermes_data head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                        symbol                   desc  chromosome      size #>                   <character>            <character> <character> <integer> #> GeneID:11185             INMT indolethylamine N-me..           7      5468 #> GeneID:10677             AVIL               advillin          12     18694 #> GeneID:101928428 LOC101928428 RNA-binding protein ..  GL000220.1       138 #> GeneID:100422835      MIR3183          microRNA 3183          17        84 #> GeneID:102466731     MIR6769A         microRNA 6769a          16        73 #> GeneID:64881           PCDH20       protocadherin 20          13      5838"},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for assert_that — assertions","title":"Additional Assertions for assert_that — assertions","text":"provide additional assertion functions can used together assertthat::assert_that().  provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional Assertions for assert_that — assertions","text":"","code":"is_class(x, class2)  is_hermes_data(x)  is_counts_vector(x)  is_list_with(x, elements)  one_provided(one, two)  is_constant(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional Assertions for assert_that — assertions","text":"x object check. class2 (character class definition) class x belong. elements (character) names elements list x. one first input. two second input.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for assert_that — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional Assertions for assert_that — assertions","text":"is_class(): checks class. is_hermes_data(): checks whether x AnyHermesData object. is_counts_vector(): checks vector counts (positive integers). is_list_with(): checks list containing elements. one_provided(): checks exactly one two inputs one, two NULL. is_constant(): checks whether vector x constant (supports numeric, factor, character, logical). NAs removed first.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/assertions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additional Assertions for assert_that — assertions","text":"","code":"# Assert a general class. a <- 5 is_class(a, \"character\") #> [1] FALSE  # Assert a `AnyHermesData` object. is_hermes_data(hermes_data) #> [1] TRUE is_hermes_data(42) #> [1] FALSE  # Assert a counts vector. a <- 5L is_counts_vector(a) #> [1] TRUE  # Assert a list containing certain elements. b <- list(a = 5, b = 3) is_list_with(b, c(\"a\", \"c\")) #> [1] FALSE is_list_with(b, c(\"a\", \"b\")) #> [1] TRUE  # Assert that exactly one of two arguments is provided. a <- 10 b <- 10 one_provided(a, b) #> [1] FALSE one_provided(a, NULL) #> [1] TRUE  # Assert a constant vector. is_constant(c(1, 2)) #> [1] FALSE is_constant(c(NA, 1)) #> [1] TRUE is_constant(c(\"a\", \"a\")) #> [1] TRUE is_constant(factor(c(\"a\", \"a\"))) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"correlate() method can calculate correlation matrix sample vectors counts specified assay. produces HermesDataCor object, extension matrix additional quality flags slot flag_data (containing tech_failure_flag low_depth_flag columns describing original input samples). autoplot() method afterwards can produce corresponding heatmap.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData correlate(object, assay_name = \"counts\", method = \"pearson\", ...)  # S4 method for HermesDataCor autoplot(   object,   flag_colors = c(`FALSE` = \"green\", `TRUE` = \"red\"),   cor_colors = circlize::colorRamp2(c(0, 0.5, 1), c(\"red\", \"yellow\", \"green\")),   ... )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"object (AnyHermesData) object calculate correlation. assay_name (string) name assay use. method (string) correlation method, see stats::cor() details. ... arguments passed ComplexHeatmap::Heatmap(). flag_colors (named character) vector specifies colors TRUE FALSE flag values. cor_colors (function) color scale function correlation values heatmap, produced circlize::colorRamp2().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"HermesDataCor object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"autoplot(HermesDataCor): autoplot() method uses ComplexHeatmap::Heatmap() function plot correlations samples saved HermesDataCor object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_cor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"","code":"object <- hermes_data  # Calculate the sample correlation matrix. correlate(object) #> An object of class \"HermesDataCor\" #>                06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> 06520011B0023R      1.0000000      0.9609738      0.6473003      0.3904017 #> 06520067C0018R      0.9609738      1.0000000      0.6758462      0.4167789 #> 06520063C0043R      0.6473003      0.6758462      1.0000000      0.7742640 #> 06520105C0017R      0.3904017      0.4167789      0.7742640      1.0000000 #> 06520092C0017R      0.6633748      0.6604377      0.6113716      0.4520703 #> 06520103C0017R      0.9079581      0.8775734      0.5978126      0.4172803 #> 06520001B0023R      0.8818454      0.8570700      0.6658466      0.5111085 #> 06520022C0017R      0.9117386      0.9142934      0.8104461      0.6131335 #> 06520062C0017R      0.6753364      0.7157011      0.8896542      0.7652040 #> 06520046C0018R      0.3208473      0.3148823      0.4431801      0.3814626 #> 06520101B0017R      0.9314543      0.9041533      0.6417565      0.4319133 #> 06520047C0017R      0.6815391      0.6707660      0.5759576      0.4652142 #> 06520024B0014R      0.5835149      0.5819907      0.6588440      0.5231136 #> 06520080B0023R      0.5168947      0.5524994      0.8949026      0.8217901 #> 06520093C0017R      0.4138013      0.4497814      0.7953623      0.7202175 #> 06520070C0018R      0.4697837      0.5046432      0.8295754      0.8553639 #> 06520023C0018R      0.4033409      0.4404680      0.8266231      0.8575140 #> 06520099B0017R      0.4224672      0.4766716      0.7936238      0.6681055 #> 06520015C0016R      0.8093514      0.8036729      0.7640655      0.6482306 #> 06520019C0023R      0.6139914      0.6389785      0.8583166      0.8280060 #>                06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> 06520011B0023R      0.6633748      0.9079581      0.8818454      0.9117386 #> 06520067C0018R      0.6604377      0.8775734      0.8570700      0.9142934 #> 06520063C0043R      0.6113716      0.5978126      0.6658466      0.8104461 #> 06520105C0017R      0.4520703      0.4172803      0.5111085      0.6131335 #> 06520092C0017R      1.0000000      0.7033489      0.6871754      0.7101840 #> 06520103C0017R      0.7033489      1.0000000      0.9863276      0.9000953 #> 06520001B0023R      0.6871754      0.9863276      1.0000000      0.9227436 #> 06520022C0017R      0.7101840      0.9000953      0.9227436      1.0000000 #> 06520062C0017R      0.5895186      0.5725651      0.6362937      0.8010688 #> 06520046C0018R      0.2638231      0.1279450      0.1317451      0.3080865 #> 06520101B0017R      0.7254041      0.9743803      0.9576231      0.9137366 #> 06520047C0017R      0.5043505      0.5349226      0.5188468      0.6281087 #> 06520024B0014R      0.4709462      0.4768380      0.5041802      0.6294704 #> 06520080B0023R      0.5609389      0.4894940      0.5836644      0.7307929 #> 06520093C0017R      0.6241234      0.4080609      0.4799501      0.6398497 #> 06520070C0018R      0.5547028      0.5587841      0.6561649      0.7291685 #> 06520023C0018R      0.5100178      0.4636074      0.5662647      0.6677198 #> 06520099B0017R      0.5000248      0.3018044      0.3613744      0.5875554 #> 06520015C0016R      0.6949487      0.9262604      0.9682275      0.9302252 #> 06520019C0023R      0.6235283      0.6475062      0.7162892      0.8016153 #>                06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> 06520011B0023R      0.6753364      0.3208473      0.9314543      0.6815391 #> 06520067C0018R      0.7157011      0.3148823      0.9041533      0.6707660 #> 06520063C0043R      0.8896542      0.4431801      0.6417565      0.5759576 #> 06520105C0017R      0.7652040      0.3814626      0.4319133      0.4652142 #> 06520092C0017R      0.5895186      0.2638231      0.7254041      0.5043505 #> 06520103C0017R      0.5725651      0.1279450      0.9743803      0.5349226 #> 06520001B0023R      0.6362937      0.1317451      0.9576231      0.5188468 #> 06520022C0017R      0.8010688      0.3080865      0.9137366      0.6281087 #> 06520062C0017R      1.0000000      0.4747608      0.6236545      0.6631752 #> 06520046C0018R      0.4747608      1.0000000      0.2381617      0.7655772 #> 06520101B0017R      0.6236545      0.2381617      1.0000000      0.6128255 #> 06520047C0017R      0.6631752      0.7655772      0.6128255      1.0000000 #> 06520024B0014R      0.6813321      0.4423075      0.5302252      0.5880107 #> 06520080B0023R      0.8997510      0.4212484      0.5343559      0.5282159 #> 06520093C0017R      0.7530101      0.3954200      0.5019182      0.4276193 #> 06520070C0018R      0.8248334      0.3424986      0.5564180      0.4850496 #> 06520023C0018R      0.8045479      0.4105629      0.4729066      0.5008448 #> 06520099B0017R      0.7839665      0.5424584      0.4246231      0.5237444 #> 06520015C0016R      0.7306067      0.1605127      0.8992993      0.5037995 #> 06520019C0023R      0.8610609      0.4903751      0.6754787      0.6867600 #>                06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> 06520011B0023R      0.5835149      0.5168947      0.4138013      0.4697837 #> 06520067C0018R      0.5819907      0.5524994      0.4497814      0.5046432 #> 06520063C0043R      0.6588440      0.8949026      0.7953623      0.8295754 #> 06520105C0017R      0.5231136      0.8217901      0.7202175      0.8553639 #> 06520092C0017R      0.4709462      0.5609389      0.6241234      0.5547028 #> 06520103C0017R      0.4768380      0.4894940      0.4080609      0.5587841 #> 06520001B0023R      0.5041802      0.5836644      0.4799501      0.6561649 #> 06520022C0017R      0.6294704      0.7307929      0.6398497      0.7291685 #> 06520062C0017R      0.6813321      0.8997510      0.7530101      0.8248334 #> 06520046C0018R      0.4423075      0.4212484      0.3954200      0.3424986 #> 06520101B0017R      0.5302252      0.5343559      0.5019182      0.5564180 #> 06520047C0017R      0.5880107      0.5282159      0.4276193      0.4850496 #> 06520024B0014R      1.0000000      0.6059874      0.5317071      0.5407754 #> 06520080B0023R      0.6059874      1.0000000      0.8384252      0.8961184 #> 06520093C0017R      0.5317071      0.8384252      1.0000000      0.7933036 #> 06520070C0018R      0.5407754      0.8961184      0.7933036      1.0000000 #> 06520023C0018R      0.5403914      0.8941102      0.8082247      0.9658703 #> 06520099B0017R      0.5677268      0.8092670      0.8884675      0.6897805 #> 06520015C0016R      0.5410291      0.7177895      0.6165727      0.8088963 #> 06520019C0023R      0.6251164      0.8780061      0.7894097      0.9381035 #>                06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> 06520011B0023R      0.4033409      0.4224672      0.8093514      0.6139914 #> 06520067C0018R      0.4404680      0.4766716      0.8036729      0.6389785 #> 06520063C0043R      0.8266231      0.7936238      0.7640655      0.8583166 #> 06520105C0017R      0.8575140      0.6681055      0.6482306      0.8280060 #> 06520092C0017R      0.5100178      0.5000248      0.6949487      0.6235283 #> 06520103C0017R      0.4636074      0.3018044      0.9262604      0.6475062 #> 06520001B0023R      0.5662647      0.3613744      0.9682275      0.7162892 #> 06520022C0017R      0.6677198      0.5875554      0.9302252      0.8016153 #> 06520062C0017R      0.8045479      0.7839665      0.7306067      0.8610609 #> 06520046C0018R      0.4105629      0.5424584      0.1605127      0.4903751 #> 06520101B0017R      0.4729066      0.4246231      0.8992993      0.6754787 #> 06520047C0017R      0.5008448      0.5237444      0.5037995      0.6867600 #> 06520024B0014R      0.5403914      0.5677268      0.5410291      0.6251164 #> 06520080B0023R      0.8941102      0.8092670      0.7177895      0.8780061 #> 06520093C0017R      0.8082247      0.8884675      0.6165727      0.7894097 #> 06520070C0018R      0.9658703      0.6897805      0.8088963      0.9381035 #> 06520023C0018R      1.0000000      0.7296291      0.7286448      0.9323267 #> 06520099B0017R      0.7296291      1.0000000      0.4846711      0.7380609 #> 06520015C0016R      0.7286448      0.4846711      1.0000000      0.8240416 #> 06520019C0023R      0.9323267      0.7380609      0.8240416      1.0000000 #> Slot \"flag_data\": #> DataFrame with 20 rows and 2 columns #>                tech_failure_flag low_depth_flag #>                        <logical>      <logical> #> 06520011B0023R             FALSE          FALSE #> 06520067C0018R             FALSE          FALSE #> 06520063C0043R             FALSE           TRUE #> 06520105C0017R             FALSE          FALSE #> 06520092C0017R             FALSE          FALSE #> ...                          ...            ... #> 06520070C0018R             FALSE          FALSE #> 06520023C0018R             FALSE          FALSE #> 06520099B0017R             FALSE          FALSE #> 06520015C0016R             FALSE          FALSE #> 06520019C0023R             FALSE          FALSE #>   # We can specify another correlation coefficient to be calculated. result <- correlate(object, method = \"spearman\")  # Plot the correlation matrix. autoplot(result)   # We can customize the heatmap. autoplot(result, show_column_names = FALSE, show_row_names = FALSE)   # Including changing the axis label text size. autoplot(   result,   row_names_gp = grid::gpar(fontsize = 8),   column_names_gp = grid::gpar(fontsize = 8) )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Principal Components Analysis Calculation — calc_pca","title":"Principal Components Analysis Calculation — calc_pca","text":"calc_pca() function performs principal components analysis gene count vectors across samples. corresponding autoplot() method can visualize results.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Principal Components Analysis Calculation — calc_pca","text":"","code":"calc_pca(object, assay_name = \"counts\", n_top = NULL)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Principal Components Analysis Calculation — calc_pca","text":"object (AnyHermesData)  input. assay_name (string)  name assay use. n_top (count NULL) filter criteria based number genes maximum variance.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Principal Components Analysis Calculation — calc_pca","text":"HermesDataPca object extension stats::prcomp class.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Principal Components Analysis Calculation — calc_pca","text":"PCA performed filtering low quality genes samples, well normalization counts. addition, genes constant counts across samples excluded analysis internally calc_pca(). Centering scaling also applied internally. Plots can obtained ggplot2::autoplot() function corresponding method ggfortify package plot results principal components analysis saved HermesDataPca object. See ggfortify::autoplot.prcomp() details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/calc_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Principal Components Analysis Calculation — calc_pca","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  result <- calc_pca(object, assay_name = \"tpm\") summary(result) #> Importance of first k=18 (out of 19) components: #>                            PC1     PC2     PC3      PC4      PC5     PC6 #> Standard deviation     22.9971 18.7315 16.3042 13.47009 13.05843 11.4881 #> Proportion of Variance  0.2212  0.1467  0.1112  0.07589  0.07132  0.0552 #> Cumulative Proportion   0.2212  0.3679  0.4791  0.55500  0.62632  0.6815 #>                             PC7     PC8     PC9    PC10    PC11    PC12    PC13 #> Standard deviation     10.60653 9.67291 9.29607 8.97324 8.54474 8.11786 7.70847 #> Proportion of Variance  0.04705 0.03913 0.03614 0.03368 0.03054 0.02756 0.02485 #> Cumulative Proportion   0.72857 0.76770 0.80384 0.83752 0.86805 0.89562 0.92047 #>                           PC14    PC15    PC16    PC17    PC18 #> Standard deviation     7.20798 6.91976 6.11309 5.77360 4.42960 #> Proportion of Variance 0.02173 0.02003 0.01563 0.01394 0.00821 #> Cumulative Proportion  0.94220 0.96222 0.97785 0.99179 1.00000  result1 <- calc_pca(object, assay_name = \"tpm\", n_top = 500) summary(result1) #> Importance of first k=18 (out of 19) components: #>                            PC1    PC2     PC3     PC4     PC5     PC6     PC7 #> Standard deviation     11.2652 9.6518 6.89353 6.34548 5.29254 5.20812 4.70857 #> Proportion of Variance  0.2538 0.1863 0.09504 0.08053 0.05602 0.05425 0.04434 #> Cumulative Proportion   0.2538 0.4401 0.53517 0.61570 0.67172 0.72597 0.77031 #>                           PC8     PC9   PC10    PC11   PC12    PC13    PC14 #> Standard deviation     4.2012 4.06409 3.7884 3.51647 3.2405 3.07753 3.04570 #> Proportion of Variance 0.0353 0.03303 0.0287 0.02473 0.0210 0.01894 0.01855 #> Cumulative Proportion  0.8056 0.83864 0.8673 0.89208 0.9131 0.93202 0.95058 #>                           PC15    PC16    PC17    PC18 #> Standard deviation     2.87077 2.65226 2.46289 1.83598 #> Proportion of Variance 0.01648 0.01407 0.01213 0.00674 #> Cumulative Proportion  0.96706 0.98113 0.99326 1.00000  # Plot the results. autoplot(result)  autoplot(result, x = 2, y = 3)  autoplot(result, variance_percentage = FALSE)  autoplot(result, label = TRUE, label.repel = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/cat_with_newline.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate and Print with Newline — cat_with_newline","title":"Concatenate and Print with Newline — cat_with_newline","text":"function concatenates inputs like cat() prints newline.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cat_with_newline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate and Print with Newline — cat_with_newline","text":"","code":"cat_with_newline(...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/cat_with_newline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate and Print with Newline — cat_with_newline","text":"... inputs concatenate.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cat_with_newline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate and Print with Newline — cat_with_newline","text":"None, used side effect producing concatenated output R console.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/cat_with_newline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Concatenate and Print with Newline — cat_with_newline","text":"","code":"cat_with_newline(\"hello\", \"world\") #> hello world"},{"path":"https://insightsengineering.github.io/hermes/main/reference/cbind.html","id":null,"dir":"Reference","previous_headings":"","what":"Column Binding of AnyHermesData Objects — cbind","title":"Column Binding of AnyHermesData Objects — cbind","text":"method combines AnyHermesData objects ranges different samples (columns assays).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cbind.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column Binding of AnyHermesData Objects — cbind","text":"... (AnyHermesData) objects column bind.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cbind.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Column Binding of AnyHermesData Objects — cbind","text":"combined AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cbind.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Column Binding of AnyHermesData Objects — cbind","text":"Note just inherits SummarizedExperiment::cbind,SummarizedExperiment-method(). binding AnyHermesData object SummarizedExperiment::SummarizedExperiment object, result SummarizedExperiment::SummarizedExperiment object (general class). Note combined object needs unique sample IDs (column names).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/cbind.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Column Binding of AnyHermesData Objects — cbind","text":"","code":"a <- hermes_data[, 1:10] b <- hermes_data[, 11:20] result <- cbind(a, b) class(result) #> [1] \"HermesData\" #> attr(,\"package\") #> [1] \"hermes\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/check_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for proportion — check_proportion","title":"Check for proportion — check_proportion","text":"Check whether x (single) proportion.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/check_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for proportion — check_proportion","text":"","code":"check_proportion(x, null.ok = FALSE)  assert_proportion(   x,   null.ok = FALSE,   .var.name = checkmate::vname(x),   add = NULL )  test_proportion(x, null.ok = FALSE)  expect_proportion(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/hermes/main/reference/check_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for proportion — check_proportion","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/check_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for proportion — check_proportion","text":"TRUE successful, otherwise string error message.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/check_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for proportion — check_proportion","text":"","code":"check_proportion(0.25) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/colMeanZscores.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean Z-score Gene Signature — colMeanZscores","title":"Mean Z-score Gene Signature — colMeanZscores","text":"helper function returns Z-score assay stored matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colMeanZscores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean Z-score Gene Signature — colMeanZscores","text":"","code":"colMeanZscores(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/colMeanZscores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean Z-score Gene Signature — colMeanZscores","text":"x (matrix) containing numeric data genes rows samples columns, missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colMeanZscores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean Z-score Gene Signature — colMeanZscores","text":"numeric vector containing mean Z-score values column x.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colMeanZscores.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean Z-score Gene Signature — colMeanZscores","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize() %>%   assay(\"counts\")  colMeanZscores(object) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>   5.195107e-04  -1.189550e-03   1.155081e-04   3.308070e-04  -1.130575e-03  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520101B0017R  #>   1.688234e-03   5.201127e-05  -1.145377e-03   1.922514e-03  -1.779591e-03  #> 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R  #>   2.320730e-04  -4.893309e-04   9.562463e-04  -3.677371e-04  -9.567040e-04  #> 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>  -5.682047e-04   7.648360e-04   2.441182e-04   8.012106e-04"},{"path":"https://insightsengineering.github.io/hermes/main/reference/colPrinComp1.html","id":null,"dir":"Reference","previous_headings":"","what":"First Principal Component (PC1) Gene Signature — colPrinComp1","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"helper function returns first principal component assay stored matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colPrinComp1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"","code":"colPrinComp1(x, center = TRUE, scale = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/colPrinComp1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"x (matrix) containing numeric data genes rows samples columns, missing values allowed. center (flag) whether variables zero centered. scale (flag) whether variables scaled unit variance.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colPrinComp1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"numeric vector containing principal component values column x.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/colPrinComp1.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize() %>%   assay(\"counts\")  colPrinComp1(object) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>    -22.7211514    -16.5888471     -8.6643020    -20.3183592     13.4998779  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520101B0017R  #>     17.9491775      4.7633163    -10.6928704    -16.1907212     30.3749930  #> 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R  #>    -25.6029134    -18.1914202     -6.9932017     36.8659028      0.7099287  #> 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>     -5.3048871     32.7696234      9.9885728      4.3472814"},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample Variables with Selected Gene Information — col_data_with_genes","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"obtains sample variables HermesData object together selected gene information.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"","code":"col_data_with_genes(object, assay_name, genes)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"object (AnyHermesData) input experiment. assay_name (string) assay use. genes (GeneSpec) genes gene signature extracted.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"combined data set, additional attribute gene_cols contains names columns obtained extracting genes information.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"class returned data set depend class colData, usually S4Vectors::DFrame.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/col_data_with_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"","code":"result <- col_data_with_genes(hermes_data, \"counts\", gene_spec(\"GeneID:1820\")) tail(names(result)) #> [1] \"COHORT\"            \"TTYPE\"             \"STDSSDY\"           #> [4] \"low_depth_flag\"    \"tech_failure_flag\" \"GeneID.1820\"       result$GeneID.1820 #>  [1]  49 153  94  54 111 567 118 171 180  16 386  57 242  73 362 144 124 243  79 #> [20] 161"},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Connection to BioMart — connect_biomart","title":"Connection to BioMart — connect_biomart","text":"connect_biomart() creates connection object class ConnectionBiomart contains biomaRt object class biomaRt::Mart prefix object used downstream query.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connection to BioMart — connect_biomart","text":"","code":"connect_biomart(prefix = c(\"ENSG\", \"GeneID\"), version = NULL)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connection to BioMart — connect_biomart","text":"prefix (string) gene ID prefix. version (string NULL) optional Ensembl version use. NULL latest available release used.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Connection to BioMart — connect_biomart","text":"ConnectionBiomart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Connection to BioMart — connect_biomart","text":"connects Ensembl data base BioMart human genes. specific version can optionally chosen ensure reproducibility results new release available, accessed data might change.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/connect_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Connection to BioMart — connect_biomart","text":"","code":"if (interactive()) {   connection <- connect_biomart(\"ENSG\") }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Control Settings for Counts Normalization — control_normalize","title":"Control Settings for Counts Normalization — control_normalize","text":"control function allows easy customization normalization settings.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control Settings for Counts Normalization — control_normalize","text":"","code":"control_normalize(   log = TRUE,   lib_sizes = NULL,   prior_count = 1,   fit_type = \"parametric\" )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control Settings for Counts Normalization — control_normalize","text":"log (flag) whether log2 values returned, otherwise original scale used. lib_sizes (NULL counts) library sizes, NULL vector sum counts samples used. prior_count (non-negative number) average count added observation avoid taking log zero, used log = TRUE. fit_type (string) method estimate dispersion parameters Negative Binomial model, used normalize() methods include vst /rlog. See estimateDispersions details.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control Settings for Counts Normalization — control_normalize","text":"List settings used perform normalization procedure.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Control Settings for Counts Normalization — control_normalize","text":"used normalize() function.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control Settings for Counts Normalization — control_normalize","text":"","code":"control_normalize() #> $log #> [1] TRUE #>  #> $lib_sizes #> NULL #>  #> $prior_count #> [1] 1 #>  #> $fit_type #> [1] \"parametric\" #>  control_normalize(log = FALSE, lib_sizes = rep(1e6L, 20)) #> $log #> [1] FALSE #>  #> $lib_sizes #>  [1] 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 #> [10] 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 #> [19] 1000000 1000000 #>  #> $prior_count #> [1] 1 #>  #> $fit_type #> [1] \"parametric\" #>"},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Control for Specified Quality Flags — control_quality","title":"Control for Specified Quality Flags — control_quality","text":"Control function specifies quality flag settings. One settings can customized. specified settings left defaults.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control for Specified Quality Flags — control_quality","text":"","code":"control_quality(   min_cpm = 1,   min_cpm_prop = 0.25,   min_corr = 0.5,   min_depth = NULL )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control for Specified Quality Flags — control_quality","text":"min_cpm (non-negative number) minimum Counts per Million (CPM) gene within sample. min_cpm_prop (proportion) minimum proportion samples acceptable CPM certain gene low expression flagging. min_corr (proportion) minimum Pearson correlation coefficient CPM samples technical failure flagging. min_depth (non-negative count NULL) minimum library depth low depth flagging. NULL, calculated first quartile minus 1.5 times inter-quartile range library size (depth) samples. (anything usual lower boxplot whisker low.)","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control for Specified Quality Flags — control_quality","text":"List criteria flag observations.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Control for Specified Quality Flags — control_quality","text":"used add_quality_flags() function.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/control_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control for Specified Quality Flags — control_quality","text":"","code":"# Default settings. control_quality() #> $min_cpm #> [1] 1 #>  #> $min_cpm_prop #> [1] 0.25 #>  #> $min_corr #> [1] 0.5 #>  #> $min_depth #> NULL #>   # One or more settings can be customized. control_quality(min_cpm = 5, min_cpm_prop = 0.001) #> $min_cpm #> [1] 5 #>  #> $min_cpm_prop #> [1] 0.001 #>  #> $min_corr #> [1] 0.5 #>  #> $min_depth #> NULL #>"},{"path":"https://insightsengineering.github.io/hermes/main/reference/correlate.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic Function for Correlation Calculations — correlate","title":"Generic Function for Correlation Calculations — correlate","text":"New generic function calculate correlations one two objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/correlate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic Function for Correlation Calculations — correlate","text":"","code":"correlate(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/correlate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic Function for Correlation Calculations — correlate","text":"object input class used decide method. ... additional arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/correlate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic Function for Correlation Calculations — correlate","text":"Corresponding object contains correlation results.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/correlate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generic Function for Correlation Calculations — correlate","text":"","code":"sample_cors <- correlate(hermes_data) autoplot(sample_cors)   pca_sample_var_cors <- correlate(calc_pca(hermes_data), hermes_data) autoplot(pca_sample_var_cors)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts Accessor and Setter — counts,AnyHermesData-method","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"methods access set counts assay AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData counts(object, ...)  # S4 method for AnyHermesData,matrix counts(object, ..., withDimnames = TRUE) <- value"},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"object (AnyHermesData) object access counts . ... used. withDimnames (flag) setting withDimnames =FALSE setter (counts<-) required dimnames supplied counts assay identical dimnames AnyHermesData object; influence actual assignment dimnames assay (always stored -). value (matrix) counts assay replaced .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"counts assay.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"counts(object = AnyHermesData) <- value:","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"","code":"a <- hermes_data result <- counts(a) class(result) #> [1] \"matrix\" \"array\"  head(result) #>                  06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:11185                  3             66             35             10 #> GeneID:10677               1668            236             95           1945 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                113             11            153             22 #>                  06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> GeneID:11185                 68            123             65             10 #> GeneID:10677                570            149            216            182 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                  0             20              1              5 #>                  06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> GeneID:11185                106             23             72              4 #> GeneID:10677                138            748            314            189 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                131            586              0            119 #>                  06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> GeneID:11185                 36              0             50            479 #> GeneID:10677                176            213            313            345 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                  9             62              0            482 #>                  06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> GeneID:11185                235             35             75             47 #> GeneID:10677               1922            269            385            687 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881               1315              0           3047            135 counts(a) <- counts(a) + 100L head(counts(a)) #>                  06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:11185                103            166            135            110 #> GeneID:10677               1768            336            195           2045 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                213            111            253            122 #>                  06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> GeneID:11185                168            223            165            110 #> GeneID:10677                670            249            316            282 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                100            120            101            105 #>                  06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> GeneID:11185                206            123            172            104 #> GeneID:10677                238            848            414            289 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                231            686            100            219 #>                  06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> GeneID:11185                136            100            150            579 #> GeneID:10677                276            313            413            445 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                109            162            100            582 #>                  06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> GeneID:11185                335            135            175            147 #> GeneID:10677               2022            369            485            787 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881               1415            100           3147            235"},{"path":"https://insightsengineering.github.io/hermes/main/reference/cut_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"function transforms numeric vector factor corresponding quantile intervals. intervals left-open right-closed.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cut_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"","code":"cut_quantile(x, percentiles = c(1/3, 2/3), digits = 0)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/cut_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"x (numeric) continuous variable values cut quantile bins. NA values taken account computing quantiles attributed NA interval. percentiles (proportions) required percentiles quantile intervals generated. Duplicated values removed. digits (integer)  precision use formatting percentages.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cut_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"factor description available quantiles levels.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/cut_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"","code":"set.seed(452) x <- runif(10, -10, 10) cut_quantile(x, c(0.33333333, 0.6666666), digits = 4) #>  [1] [0%,33.3333%]       (33.3333%,66.6667%] [0%,33.3333%]       #>  [4] (66.6667%,100%]     (33.3333%,66.6667%] [0%,33.3333%]       #>  [7] (66.6667%,100%]     (33.3333%,66.6667%] (33.3333%,66.6667%] #> [10] (66.6667%,100%]     #> Levels: [0%,33.3333%] (33.3333%,66.6667%] (66.6667%,100%]  x[1:4] <- NA cut_quantile(x) #>  [1] <NA>       <NA>       <NA>       <NA>       (33%,67%]  [0%,33%]   #>  [7] (67%,100%] (33%,67%]  [0%,33%]   (67%,100%] #> Levels: [0%,33%] (33%,67%] (67%,100%]"},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"utility function converts eligible character logical variables S4Vectors::DataFrame factor variables. factor variables get amended explicit missing level. includes NA empty strings.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"","code":"df_cols_to_factor(data, omit_columns = NULL, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"data (DataFrame) input S4Vectors::DataFrame. omit_columns (character NULL) columns omitted possible conversion factor explicit missing level application. na_level (string) explicit missing level used factor variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"modified data.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"required rowData colData variables converted ensure proper downstream behavior. automatically omitted found data therefore need specified omit_columns.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/df_cols_to_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"","code":"dat <- colData(summarized_experiment) any(vapply(dat, is.character, logical(1))) #> [1] TRUE any(vapply(dat, is.logical, logical(1))) #> [1] TRUE dat_converted <- df_cols_to_factor(dat) any(vapply(dat_converted, function(x) is.character(x) || is.logical(x), logical(1))) #> [1] FALSE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential Expression Analysis — diff_expression","title":"Differential Expression Analysis — diff_expression","text":"diff_expression() function performs differential expression analysis using method preference. corresponding autoplot() method visualizing results volcano plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential Expression Analysis — diff_expression","text":"","code":"diff_expression(object, group, method = c(\"voom\", \"deseq2\"), ...)  # S4 method for HermesDataDiffExpr autoplot(object, adj_p_val_thresh = 0.05, log2_fc_thresh = 2.5)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential Expression Analysis — diff_expression","text":"object (AnyHermesData) input. Note function uses original counts analysis, need normalized. group (string) name factor variable 2 levels colData(object). 2 levels compared differential expression analysis. method (string) method differential expression analysis, see details . ... additional arguments passed helper function associated selected method. adj_p_val_thresh (proportion) threshold adjusted p-values (y-axis) flag significance. log2_fc_thresh (number) threshold absolute log2 fold-change (x-axis) flag - -regulation transcription.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential Expression Analysis — diff_expression","text":"HermesDataDiffExpr object data frame following columns gene HermesData object: log2_fc (estimate log2 fold change 2 levels provided factor) stat (test statistic, one depends method used) p_val (raw p-value) adj_p_val (multiplicity adjusted p-value value)","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Differential Expression Analysis — diff_expression","text":"Possible method choices : voom: uses limma::voom(), see h_diff_expr_voom() details. deseq2: uses DESeq2::DESeq(), see h_diff_expr_deseq2() details.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Differential Expression Analysis — diff_expression","text":"autoplot(HermesDataDiffExpr): generates volcano plot HermesDataDiffExpr object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Differential Expression Analysis — diff_expression","text":"provide df_cols_to_factor() utility function makes easy convert colData() character logical variables factors, can subsequently used group inputs. See example. order avoid warning using deseq2, can necessary specify fitType = \"local\" additional argument. e.g. case samples present case default parametric dispersions estimation work.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/diff_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Differential Expression Analysis — diff_expression","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter()  # Convert character and logical to factor variables in `colData`, # including the below used `group` variable. colData(object) <- df_cols_to_factor(colData(object)) res1 <- diff_expression(object, group = \"SEX\", method = \"voom\") head(res1) #>                  log2_fc      stat       p_val adj_p_val #> GeneID:344558  1.4951365  3.768257 0.001217934 0.7815544 #> GeneID:51227  -1.0670584 -3.766113 0.001224023 0.7815544 #> GeneID:10280  -0.7518694 -3.461800 0.002478362 0.7815544 #> GeneID:9435    1.8555120  3.414364 0.002764727 0.7815544 #> GeneID:51575  -0.7238103 -3.326330 0.003384750 0.7815544 #> GeneID:123036  2.8900474  3.246333 0.004064925 0.7815544 res2 <- diff_expression(object, group = \"SEX\", method = \"deseq2\") head(res2) #>                  log2_fc      stat        p_val   adj_p_val #> GeneID:64344  -2.9129064 -4.864176 1.149347e-06 0.002694069 #> GeneID:9002    2.3092323  4.215740 2.489604e-05 0.020061145 #> GeneID:167681 -4.0974632 -4.201788 2.648146e-05 0.020061145 #> GeneID:51227  -1.1573425 -4.143302 3.423404e-05 0.020061145 #> GeneID:4359    2.8926465  4.004010 6.227765e-05 0.029195764 #> GeneID:10280  -0.7997803 -3.876433 1.059991e-04 0.031057749  # Pass method arguments to the internally used helper functions. res3 <- diff_expression(object, group = \"SEX\", method = \"voom\", robust = TRUE, trend = TRUE) head(res3) #>                  log2_fc      stat       p_val adj_p_val #> GeneID:51227  -1.0670584 -3.765145 0.001226726 0.7884829 #> GeneID:344558  1.4951365  3.759186 0.001243851 0.7884829 #> GeneID:10280  -0.7518694 -3.467915 0.002443545 0.7884829 #> GeneID:9435    1.8555120  3.390300 0.002922073 0.7884829 #> GeneID:51575  -0.7238103 -3.325713 0.003389426 0.7884829 #> GeneID:123036  2.8900474  3.232786 0.004230256 0.7884829 res4 <- diff_expression(object, group = \"SEX\", method = \"deseq2\", fitType = \"local\") head(res4) #>                  log2_fc      stat        p_val   adj_p_val #> GeneID:64344  -2.9128847 -4.892128 9.975152e-07 0.002338176 #> GeneID:9002    2.3091854  4.256818 2.073572e-05 0.014702529 #> GeneID:167681 -4.0975071 -4.300519 1.703986e-05 0.014702529 #> GeneID:51227  -1.1573487 -4.213992 2.508964e-05 0.014702529 #> GeneID:4359    2.8925392  4.055798 4.996349e-05 0.021309899 #> GeneID:10280  -0.7997974 -3.958566 7.540117e-05 0.021309899  # Create the corresponding volcano plots. autoplot(res1)  autoplot(res3)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Barplot for Gene Expression Percentiles — draw_barplot","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"produces barplot dichotomized gene expression counts two three categories based custom defined percentiles.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"","code":"draw_barplot(   object,   assay_name,   x_spec,   facet_var = NULL,   fill_var = NULL,   percentiles = c(1/3, 2/3) )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input. x_spec (GeneSpec) gene specification x-axis. facet_var (string NULL) optional faceting variable, taken input sample variables. fill_var (string NULL) optional fill variable, taken input sample variables. percentiles (vector) lower upper percentiles dichotomize gene counts two three categories.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"ggplot barplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"","code":"object <- hermes_data  g <- genes(object)  draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1]),   facet_var = \"SEX\",   fill_var = \"AGE18\" )   draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1:3], colMedians, \"Median\"),   facet_var = \"SEX\",   fill_var = \"AGE18\" )   draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1:3], colMeans, \"Mean\"),   facet_var = \"SEX\",   fill_var = \"AGE18\",   percentiles = c(0.1, 0.9) )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Boxplot for Gene Expression Values — draw_boxplot","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"produces boxplots gene expression values single gene, multiple genes gene signature.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"","code":"draw_boxplot(   object,   assay_name,   genes,   x_var = NULL,   color_var = NULL,   facet_var = NULL,   violin = FALSE,   jitter = FALSE )  h_draw_boxplot_df(object, assay_name, genes, x_var, color_var, facet_var)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input y-axis. genes (GeneSpec) genes gene signature produce boxplots. x_var (string NULL) optional stratifying variable x-axis, taken input sample variables. color_var (string NULL) optional color variable, taken input sample variables. facet_var (string NULL) optional faceting variable, taken input sample variables. violin (flag) whether draw violin plot instead boxplot. jitter (flag) whether add jittered original data points.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"ggplot boxplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"h_draw_boxplot_df(): Helper function prepare data frame required plotting.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"","code":"object <- hermes_data draw_boxplot(   object,   assay_name = \"counts\",   genes = gene_spec(c(A = genes(object)[1])),   violin = TRUE )   object2 <- object %>%   add_quality_flags() %>%   filter() %>%   normalize() draw_boxplot(   object2,   assay_name = \"tpm\",   x_var = \"SEX\",   genes = gene_spec(setNames(genes(object2)[1:10], 1:10), fun = colMeans),   facet_var = \"RACE\",   color_var = \"AGE18\",   jitter = TRUE )   draw_boxplot(   object,   assay_name = \"counts\",   x_var = \"SEX\",   genes = gene_spec(genes(object)[1:3]),   jitter = TRUE,   facet_var = \"AGE18\" )   draw_boxplot(   object,   assay_name = \"counts\",   genes = gene_spec(c(A = \"GeneID:11185\", B = \"GeneID:10677\")),   violin = TRUE )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_genes_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"creates barplot chromosomes AnyHermesData object proportions low expression genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_genes_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"","code":"draw_genes_barplot(   object,   chromosomes = c(seq_len(22), \"X\", \"Y\", \"MT\"),   include_others = TRUE )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_genes_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"object (AnyHermesData) input. chromosomes (character) names chromosomes displayed. include_others (flag) option show chromosomes chromosomes \"Others\".","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_genes_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"ggplot object histogram.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_genes_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"","code":"object <- hermes_data  # Display chromosomes 1-22, X, Y, and MT. Other chromosomes are displayed in \"Others\". # To increase readability, we can have flip the coordinate axes. draw_genes_barplot(object) + coord_flip()   # Alternatively we can also rotate the x-axis tick labels. draw_genes_barplot(object) + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))   # Display chromosomes 1 and 2. Other chromosomes are displayed in \"Others\". draw_genes_barplot(object, chromosomes = c(\"1\", \"2\"))   # Display chromosomes 1 and 2 only. draw_genes_barplot(object, chromosomes = c(\"1\", \"2\"), include_others = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_heatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Heatmap for Gene Expression Counts — draw_heatmap","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"produces heatmap chosen assay groups various sample variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_heatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"","code":"draw_heatmap(   object,   assay_name,   color_extremes = c(0.01, 0.99),   col_data_annotation = NULL,   ... )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_heatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"object (AnyHermesData) input. assay_name (string) selects assay input. color_extremes (numeric) min max percentiles inform color scheme heatmap blue red respectively. col_data_annotation (character NULL) optional grouping variable(s), taken input sample variables. ... additional arguments pass ComplexHeatmap::Heatmap().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_heatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"ComplexHeatmap::Heatmap heatmap","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_heatmap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"","code":"result <- hermes_data %>%   normalize(methods = \"voom\") %>%   add_quality_flags() %>%   filter(what = \"genes\")  draw_heatmap(   object = result[1:10, ],   assay_name = \"counts\",   col_data_annotation = \"COUNTRY\" )   draw_heatmap(   object = result[1:10, ],   assay_name = \"counts\",   color_extremes = c(0.001, 0.999),   col_data_annotation = \"AGEGRP\" )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_densities.html","id":null,"dir":"Reference","previous_headings":"","what":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"creates density plot (log) counts distributions AnyHermesData object line plot corresponds sample.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_densities.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"","code":"draw_libsize_densities(object, log = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_densities.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"object (AnyHermesData) input. log (flag) counts log transformed (log2).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_densities.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"ggplot object density plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_densities.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"","code":"result <- hermes_data draw_libsize_densities(result)  draw_libsize_densities(result, log = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_hist.html","id":null,"dir":"Reference","previous_headings":"","what":"Histogram of Library Sizes — draw_libsize_hist","title":"Histogram of Library Sizes — draw_libsize_hist","text":"creates histogram library sizes AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_hist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Histogram of Library Sizes — draw_libsize_hist","text":"","code":"draw_libsize_hist(object, bins = 30L, fill = \"darkgrey\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_hist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Histogram of Library Sizes — draw_libsize_hist","text":"object (AnyHermesData) input. bins (count) number evenly distributed groups desired. fill (string) color bars filling.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_hist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Histogram of Library Sizes — draw_libsize_hist","text":"ggplot object histogram.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_hist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Histogram of Library Sizes — draw_libsize_hist","text":"","code":"result <- hermes_data draw_libsize_hist(result)  draw_libsize_hist(result, bins = 10L, fill = \"blue\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_qq.html","id":null,"dir":"Reference","previous_headings":"","what":"Q-Q Plot of Library Sizes — draw_libsize_qq","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"creates Q-Q plot library sizes AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_qq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"","code":"draw_libsize_qq(object, color = \"grey\", linetype = \"dashed\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_qq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"object (AnyHermesData) input. color (string) color Q-Q line. linetype (string) line type  Q-Q line.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_qq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"ggplot object Q-Q Plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_libsize_qq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"","code":"result <- hermes_data draw_libsize_qq(result)  draw_libsize_qq(result, color = \"blue\", linetype = \"solid\")   # We can also add sample names as labels. library(ggrepel) draw_libsize_qq(result) + geom_text_repel(label = colnames(result), stat = \"qq\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_nonzero_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"draws boxplot, overlaid data points, number non-zero expressed genes per sample.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_nonzero_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"","code":"draw_nonzero_boxplot(object, position = position_jitter(0.2), alpha = 0.25)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_nonzero_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"object (AnyHermesData) input. position (Position) specifies x-axis position points, e.g. jittering. alpha (proportion) specifies transparency points.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_nonzero_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"ggplot object boxplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_nonzero_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"","code":"# Default boxplot. result <- hermes_data draw_nonzero_boxplot(result)   # Reusing the same position for labeling. library(ggrepel) pos <- position_jitter(0.5) draw_nonzero_boxplot(result, position = pos) +   geom_text_repel(aes(label = samples(result)), position = pos)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatterplot for Gene Expression Values — draw_scatterplot","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"produces scatterplot two genes gene signatures.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"","code":"draw_scatterplot(   object,   assay_name,   x_spec,   y_spec,   color_var = NULL,   facet_var = NULL,   smooth_method = c(\"lm\", \"loess\", \"none\") )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input. x_spec (GeneSpec) gene specification x-axis. y_spec (GeneSpec) gene specification y-axis. color_var (string NULL) optional color variable, taken input sample variables. facet_var (string NULL) optional faceting variable, taken input sample variables. smooth_method (string) smoothing method use, either linear regression line (lm), local polynomial regression (loess) none.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"ggplot scatterplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/draw_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"","code":"object <- hermes_data g <- genes(object)  draw_scatterplot(   object,   assay_name = \"counts\",   facet_var = NULL,   x_spec = gene_spec(c(A = g[1])),   y_spec = gene_spec(g[2]),   color = \"RACE\" )   object2 <- object %>%   add_quality_flags() %>%   filter() %>%   normalize() g2 <- genes(object2)  draw_scatterplot(   object2,   assay_name = \"tpm\",   facet_var = \"SEX\",   x_spec = gene_spec(g2[1:10], colMeans, \"Mean\"),   y_spec = gene_spec(g2[11:20], colMedians, \"Median\"),   smooth_method = \"loess\" )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/expression_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Example ExpressionSet Data — expression_set","title":"Example ExpressionSet Data — expression_set","text":"example data can used try conversion Biobase::ExpressionSet object HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/expression_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example ExpressionSet Data — expression_set","text":"","code":"expression_set"},{"path":"https://insightsengineering.github.io/hermes/main/reference/expression_set.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example ExpressionSet Data — expression_set","text":"Biobase::ExpressionSet object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/expression_set.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example ExpressionSet Data — expression_set","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/extra_data_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Extra Variable Names Accessor Methods — extra_data_names","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"methods access names variables colData() rowData() object required design. can additional sample patient characteristics, gene characteristics.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/extra_data_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"","code":"extraColDataNames(x, ...)  # S4 method for AnyHermesData extraColDataNames(x, ...)  extraRowDataNames(x, ...)  # S4 method for AnyHermesData extraRowDataNames(x, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/extra_data_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"x (AnyHermesData) object. ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/extra_data_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"character vector additional variable names either colData() rowData().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/extra_data_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"","code":"object <- hermes_data extraColDataNames(object) #>  [1] \"Filename\" \"SampleID\" \"AGEGRP\"   \"AGE18\"    \"STDDRS\"   \"STDDRSD\"  #>  [7] \"STDSSDT\"  \"TRTDRS\"   \"TRTDRSD\"  \"BHDCIRC\"  \"BHDCIRCU\" \"ADAFL\"    #> [13] \"BLANP\"    \"BKPS\"     \"BLKS\"     \"BTANNER\"  \"FRPST\"    \"DURIDX\"   #> [19] \"DURSAF\"   \"DURSUR\"   \"LNTHRPY\"  \"AENCIFL\"  \"STUDYID\"  \"USUBJID\"  #> [25] \"RFSTDTC\"  \"RFENDTC\"  \"RFXSTDTC\" \"RFXENDTC\" \"RFICDTC\"  \"RFPENDTC\" #> [31] \"DTHDTC\"   \"DTHFL\"    \"SITEID\"   \"INVID\"    \"AGE\"      \"AGEU\"     #> [37] \"SEX\"      \"RACE\"     \"ETHNIC\"   \"ARMCD\"    \"ARM\"      \"ACTARMCD\" #> [43] \"ACTARM\"   \"COUNTRY\"  \"DMDTC\"    \"DMDY\"     \"BAGE\"     \"BAGEU\"    #> [49] \"BWT\"      \"BWTU\"     \"BHT\"      \"BHTU\"     \"BBMI\"     \"ITTFL\"    #> [55] \"SAFFL\"    \"INFCODT\"  \"RANDDT\"   \"TRTSDTC\"  \"TRTSDTM\"  \"TRTSTMF\"  #> [61] \"TRTEDTM\"  \"TRTETMF\"  \"TRTDUR\"   \"DISCSTUD\" \"DISCDEAT\" \"DISCAE\"   #> [67] \"DISTRTFL\" \"AEWITHFL\" \"ALIVDT\"   \"COHORT\"   \"TTYPE\"    \"STDSSDY\"  extraRowDataNames(object) #> [1] \"GeneID\"          \"SYMBOL\"          \"chromosome_name\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"filters AnyHermesData object using default QC flags required annotations.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"","code":"filter(object, ...)  # S4 method for AnyHermesData filter(object, what = c(\"genes\", \"samples\"), annotation_required = \"size\")  # S4 method for data.frame filter(object, ...)  # S4 method for ts filter(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"object (AnyHermesData) object filter. ... additional arguments. (character) specify whether apply filter genes / samples. annotation_required (character) names required annotation columns genes. used genes filtered.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"filtered AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"genes without low expression (low_expression_flag) samples without low depth (low_depth_flag) technical failure (tech_failure_flag) remain returned filtered object. Also required gene annotation columns can specified, genes complete columns filtered . default size column, needed default normalization object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"internal implementation use subset() method since requires non-standard evaluation arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"","code":"a <- hermes_data dim(a) #> [1] 5085   20  # Filter genes and samples on default QC flags. result <- filter(a) dim(result) #> [1] 2064   18  # Filter only genes without low expression. result <- filter(a, what = \"genes\")  # Filter only samples with low depth and technical failure. result <- filter(a, what = \"samples\")  # Filter only genes, and require certain annotations to be present. result <- filter(a, what = \"genes\", annotation_required = c(\"size\"))"},{"path":"https://insightsengineering.github.io/hermes/main/reference/gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"GeneSpec Constructor — gene_spec","title":"GeneSpec Constructor — gene_spec","text":"Creates new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GeneSpec Constructor — gene_spec","text":"","code":"gene_spec(genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))"},{"path":"https://insightsengineering.github.io/hermes/main/reference/gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GeneSpec Constructor — gene_spec","text":"genes (named character NULL) gene IDs, names used labels available. fun (function NULL) summary function. NULL used multiple genes summarized returned matrix extract method. fun_name (string) name summary function.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/gene_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GeneSpec Constructor — gene_spec","text":"new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/gene_spec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GeneSpec Constructor — gene_spec","text":"","code":"gene_spec(\"GeneID:11185\") #> <GeneSpec> #>   Public: #>     clone: function (deep = FALSE)  #>     extract: function (assay)  #>     extract_data_frame: function (assay)  #>     get_gene_labels: function (genes = self$get_genes())  #>     get_genes: function ()  #>     get_label: function (genes = self$get_genes())  #>     initialize: function (genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))  #>     returns_vector: function ()  #>   Private: #>     fun: NULL #>     fun_name: NULL #>     gene_labels: GeneID:11185 #>     genes: GeneID:11185 gene_spec(c(\"GeneID:11185\", \"GeneID:10677\", \"GeneID:101928428\"), fun = colMeans) #> <GeneSpec> #>   Public: #>     clone: function (deep = FALSE)  #>     extract: function (assay)  #>     extract_data_frame: function (assay)  #>     get_gene_labels: function (genes = self$get_genes())  #>     get_genes: function ()  #>     get_label: function (genes = self$get_genes())  #>     initialize: function (genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))  #>     returns_vector: function ()  #>   Private: #>     fun: function (x, na.rm = FALSE, dims = 1, ...)  #>     fun_name: colMeans #>     gene_labels: GeneID:11185 GeneID:10677 GeneID:101928428 #>     genes: GeneID:11185 GeneID:10677 GeneID:101928428"},{"path":"https://insightsengineering.github.io/hermes/main/reference/genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Gene IDs Accessor — genes","title":"Gene IDs Accessor — genes","text":"Access gene IDs, .e. row names, AnyHermesData object nicely named accessor method.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gene IDs Accessor — genes","text":"","code":"genes(object)  # S4 method for AnyHermesData genes(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gene IDs Accessor — genes","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gene IDs Accessor — genes","text":"character vector gene IDs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gene IDs Accessor — genes","text":"","code":"a <- hermes_data genes(a) #>    [1] \"GeneID:11185\"     \"GeneID:10677\"     \"GeneID:101928428\" #>    [4] \"GeneID:100422835\" \"GeneID:102466731\" \"GeneID:64881\"     #>    [7] \"GeneID:286205\"    \"GeneID:8365\"      \"GeneID:6804\"      #>   [10] \"GeneID:100423018\" \"GeneID:23526\"     \"GeneID:102724693\" #>   [13] \"GeneID:10755\"     \"GeneID:283150\"    \"GeneID:101929282\" #>   [16] \"GeneID:57630\"     \"GeneID:101930284\" \"GeneID:102724480\" #>   [19] \"GeneID:9724\"      \"GeneID:647166\"    \"GeneID:339010\"    #>   [22] \"GeneID:4595\"      \"GeneID:11019\"     \"GeneID:407020\"    #>   [25] \"GeneID:116154\"    \"GeneID:27336\"     \"GeneID:51455\"     #>   [28] \"GeneID:26225\"     \"GeneID:102723987\" \"GeneID:5828\"      #>   [31] \"GeneID:100533181\" \"GeneID:10940\"     \"GeneID:55290\"     #>   [34] \"GeneID:2790\"      \"GeneID:101928197\" \"GeneID:277\"       #>   [37] \"GeneID:26818\"     \"GeneID:574033\"    \"GeneID:101929014\" #>   [40] \"GeneID:7200\"      \"GeneID:7386\"      \"GeneID:100422893\" #>   [43] \"GeneID:11189\"     \"GeneID:100130331\" \"GeneID:102723828\" #>   [46] \"GeneID:54936\"     \"GeneID:1088\"      \"GeneID:283234\"    #>   [49] \"GeneID:100505495\" \"GeneID:345462\"    \"GeneID:101927039\" #>   [52] \"GeneID:79908\"     \"GeneID:100130673\" \"GeneID:6277\"      #>   [55] \"GeneID:100846993\" \"GeneID:284836\"    \"GeneID:151827\"    #>   [58] \"GeneID:100507616\" \"GeneID:112812\"    \"GeneID:51098\"     #>   [61] \"GeneID:84278\"     \"GeneID:256643\"    \"GeneID:101927809\" #>   [64] \"GeneID:3149\"      \"GeneID:101929908\" \"GeneID:80201\"     #>   [67] \"GeneID:1553\"      \"GeneID:10966\"     \"GeneID:101928449\" #>   [70] \"GeneID:80024\"     \"GeneID:101928694\" \"GeneID:80305\"     #>   [73] \"GeneID:101927496\" \"GeneID:101927407\" \"GeneID:100996349\" #>   [76] \"GeneID:283624\"    \"GeneID:1057\"      \"GeneID:100287205\" #>   [79] \"GeneID:10919\"     \"GeneID:5686\"      \"GeneID:100302242\" #>   [82] \"GeneID:3454\"      \"GeneID:102725213\" \"GeneID:101930449\" #>   [85] \"GeneID:101927483\" \"GeneID:114770\"    \"GeneID:101928266\" #>   [88] \"GeneID:101927348\" \"GeneID:222894\"    \"GeneID:100316904\" #>   [91] \"GeneID:55128\"     \"GeneID:100874195\" \"GeneID:8685\"      #>   [94] \"GeneID:101927044\" \"GeneID:102466738\" \"GeneID:8295\"      #>   [97] \"GeneID:85456\"     \"GeneID:102725169\" \"GeneID:101927105\" #>  [100] \"GeneID:643355\"    \"GeneID:56931\"     \"GeneID:8354\"      #>  [103] \"GeneID:9717\"      \"GeneID:85016\"     \"GeneID:26222\"     #>  [106] \"GeneID:102725324\" \"GeneID:102724216\" \"GeneID:27333\"     #>  [109] \"GeneID:26999\"     \"GeneID:11212\"     \"GeneID:9024\"      #>  [112] \"GeneID:4359\"      \"GeneID:101927249\" \"GeneID:2055\"      #>  [115] \"GeneID:8325\"      \"GeneID:253982\"    \"GeneID:81544\"     #>  [118] \"GeneID:390067\"    \"GeneID:4261\"      \"GeneID:7472\"      #>  [121] \"GeneID:27299\"     \"GeneID:9383\"      \"GeneID:113730\"    #>  [124] \"GeneID:25984\"     \"GeneID:134265\"    \"GeneID:4141\"      #>  [127] \"GeneID:56651\"     \"GeneID:345456\"    \"GeneID:932\"       #>  [130] \"GeneID:3690\"      \"GeneID:22848\"     \"GeneID:102723454\" #>  [133] \"GeneID:100616330\" \"GeneID:7171\"      \"GeneID:102723659\" #>  [136] \"GeneID:9473\"      \"GeneID:391123\"    \"GeneID:9811\"      #>  [139] \"GeneID:147525\"    \"GeneID:338817\"    \"GeneID:219874\"    #>  [142] \"GeneID:3653\"      \"GeneID:221120\"    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\"GeneID:102725434\" #> [1867] \"GeneID:101926955\" \"GeneID:9537\"      \"GeneID:117145\"    #> [1870] \"GeneID:101928323\" \"GeneID:88\"        \"GeneID:101929654\" #> [1873] \"GeneID:388387\"    \"GeneID:64747\"     \"GeneID:101927082\" #> [1876] \"GeneID:5141\"      \"GeneID:100034743\" \"GeneID:441932\"    #> [1879] \"GeneID:222389\"    \"GeneID:5860\"      \"GeneID:102465506\" #> [1882] \"GeneID:27248\"     \"GeneID:3284\"      \"GeneID:55713\"     #> [1885] \"GeneID:101929478\" \"GeneID:2017\"      \"GeneID:5648\"      #> [1888] \"GeneID:65061\"     \"GeneID:26019\"     \"GeneID:7037\"      #> [1891] \"GeneID:51725\"     \"GeneID:100874531\" \"GeneID:101928098\" #> [1894] \"GeneID:22853\"     \"GeneID:158055\"    \"GeneID:3651\"      #> [1897] \"GeneID:390066\"    \"GeneID:102723375\" \"GeneID:2267\"      #> [1900] \"GeneID:387129\"    \"GeneID:7994\"      \"GeneID:79869\"     #> [1903] \"GeneID:100169959\" \"GeneID:102723382\" \"GeneID:55753\"     #> [1906] \"GeneID:100616476\" \"GeneID:25825\"     \"GeneID:100996465\" #> [1909] \"GeneID:6100\"      \"GeneID:651\"       \"GeneID:221584\"    #> [1912] \"GeneID:101928144\" \"GeneID:100036566\" \"GeneID:56729\"     #> [1915] \"GeneID:407027\"    \"GeneID:3911\"      \"GeneID:8890\"      #> [1918] \"GeneID:54620\"     \"GeneID:101928136\" \"GeneID:100500876\" #> [1921] \"GeneID:102723862\" \"GeneID:101927378\" \"GeneID:266\"       #> [1924] \"GeneID:102725009\" \"GeneID:84647\"     \"GeneID:102724492\" #> [1927] \"GeneID:3008\"      \"GeneID:3682\"      \"GeneID:101928220\" #> [1930] \"GeneID:26083\"     \"GeneID:8310\"      \"GeneID:1427\"      #> [1933] \"GeneID:10950\"     \"GeneID:647264\"    \"GeneID:101929657\" #> [1936] \"GeneID:5566\"      \"GeneID:100874127\" \"GeneID:9231\"      #> [1939] \"GeneID:102723687\" \"GeneID:284618\"    \"GeneID:8345\"      #> [1942] \"GeneID:440051\"    \"GeneID:58505\"     \"GeneID:9266\"      #> [1945] \"GeneID:55500\"     \"GeneID:6888\"      \"GeneID:285740\"    #> [1948] \"GeneID:102724326\" \"GeneID:3630\"      \"GeneID:158747\"    #> [1951] \"GeneID:51447\"     \"GeneID:57608\"     \"GeneID:3304\"      #> [1954] \"GeneID:728339\"    \"GeneID:286319\"    \"GeneID:677784\"    #> [1957] \"GeneID:613126\"    \"GeneID:25865\"     \"GeneID:1783\"      #> [1960] \"GeneID:79025\"     \"GeneID:3442\"      \"GeneID:102725307\" #> [1963] \"GeneID:101928955\" \"GeneID:9162\"      \"GeneID:79609\"     #> [1966] \"GeneID:28\"        \"GeneID:729862\"    \"GeneID:3754\"      #> [1969] \"GeneID:100302143\" \"GeneID:100532742\" \"GeneID:154754\"    #> [1972] \"GeneID:100422912\" \"GeneID:50840\"     \"GeneID:25774\"     #> [1975] \"GeneID:442721\"    \"GeneID:5438\"      \"GeneID:55738\"     #> [1978] \"GeneID:9592\"      \"GeneID:10849\"     \"GeneID:374860\"    #> [1981] \"GeneID:100996588\" \"GeneID:101929229\" \"GeneID:375316\"    #> [1984] \"GeneID:342666\"    \"GeneID:100506241\" \"GeneID:4879\"      #> [1987] \"GeneID:5370\"      \"GeneID:100137049\" \"GeneID:55079\"     #> [1990] \"GeneID:123036\"    \"GeneID:100287171\" \"GeneID:79026\"     #> [1993] \"GeneID:6003\"      \"GeneID:101929019\" \"GeneID:1522\"      #> [1996] \"GeneID:130497\"    \"GeneID:102723671\" \"GeneID:5173\"      #> [1999] \"GeneID:4223\"      \"GeneID:102724949\" \"GeneID:6996\"      #> [2002] \"GeneID:645027\"    \"GeneID:79171\"     \"GeneID:84898\"     #> [2005] \"GeneID:100996669\" \"GeneID:7139\"      \"GeneID:10933\"     #> [2008] \"GeneID:102725095\" \"GeneID:285533\"    \"GeneID:8711\"      #> [2011] \"GeneID:26774\"     \"GeneID:27247\"     \"GeneID:10844\"     #> [2014] \"GeneID:8634\"      \"GeneID:100128573\" \"GeneID:1802\"      #> [2017] \"GeneID:140886\"    \"GeneID:120065\"    \"GeneID:101060216\" #> [2020] \"GeneID:84931\"     \"GeneID:25987\"     \"GeneID:333929\"    #> [2023] \"GeneID:101929552\" \"GeneID:83606\"     \"GeneID:212\"       #> [2026] \"GeneID:83756\"     \"GeneID:102465517\" \"GeneID:121536\"    #> [2029] \"GeneID:11258\"     \"GeneID:283981\"    \"GeneID:9969\"      #> [2032] \"GeneID:3360\"      \"GeneID:723805\"    \"GeneID:187\"       #> [2035] \"GeneID:55175\"     \"GeneID:645520\"    \"GeneID:150696\"    #> [2038] \"GeneID:29085\"     \"GeneID:100874372\" \"GeneID:3126\"      #> [2041] \"GeneID:643770\"    \"GeneID:284294\"    \"GeneID:100507855\" #> [2044] \"GeneID:102466250\" \"GeneID:101060181\" \"GeneID:80196\"     #> [2047] \"GeneID:101930479\" \"GeneID:129531\"    \"GeneID:101928257\" #> [2050] \"GeneID:100422996\" \"GeneID:101928870\" \"GeneID:100847022\" #> [2053] \"GeneID:6948\"      \"GeneID:101928811\" \"GeneID:219790\"    #> [2056] \"GeneID:57498\"     \"GeneID:102467214\" \"GeneID:388697\"    #> [2059] \"GeneID:54657\"     \"GeneID:102724766\" \"GeneID:3043\"      #> [2062] \"GeneID:100268168\" \"GeneID:10090\"     \"GeneID:23276\"     #> [2065] \"GeneID:102724798\" \"GeneID:9846\"      \"GeneID:493856\"    #> [2068] \"GeneID:100033799\" \"GeneID:8204\"      \"GeneID:102725481\" #> [2071] 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\"GeneID:1592\"      \"GeneID:102723342\" \"GeneID:29904\"     #> [2812] \"GeneID:326625\"    \"GeneID:84957\"     \"GeneID:83877\"     #> [2815] \"GeneID:825\"       \"GeneID:1747\"      \"GeneID:728276\"    #> [2818] \"GeneID:57701\"     \"GeneID:401563\"    \"GeneID:102723354\" #> [2821] \"GeneID:100500884\" \"GeneID:266747\"    \"GeneID:90523\"     #> [2824] \"GeneID:92312\"     \"GeneID:4705\"      \"GeneID:200845\"    #> [2827] \"GeneID:284001\"    \"GeneID:103752555\" \"GeneID:8260\"      #> [2830] \"GeneID:100126306\" \"GeneID:93550\"     \"GeneID:714\"       #> [2833] \"GeneID:220382\"    \"GeneID:102723831\" \"GeneID:5213\"      #> [2836] \"GeneID:57452\"     \"GeneID:8986\"      \"GeneID:54908\"     #> [2839] \"GeneID:388015\"    \"GeneID:100329135\" \"GeneID:4828\"      #> [2842] \"GeneID:408187\"    \"GeneID:57577\"     \"GeneID:102465906\" #> [2845] \"GeneID:4900\"      \"GeneID:8439\"      \"GeneID:3087\"      #> [2848] \"GeneID:158056\"    \"GeneID:83547\"     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\"GeneID:3081\"      \"GeneID:729506\"    \"GeneID:100126330\" #> [4165] \"GeneID:643802\"    \"GeneID:57699\"     \"GeneID:440993\"    #> [4168] \"GeneID:574460\"    \"GeneID:9630\"      \"GeneID:101929183\" #> [4171] \"GeneID:56254\"     \"GeneID:4322\"      \"GeneID:54476\"     #> [4174] \"GeneID:84321\"     \"GeneID:55231\"     \"GeneID:400797\"    #> [4177] \"GeneID:5676\"      \"GeneID:100874155\" \"GeneID:9343\"      #> [4180] \"GeneID:101927297\" \"GeneID:124411\"    \"GeneID:9825\"      #> [4183] \"GeneID:85452\"     \"GeneID:101927137\" \"GeneID:101928819\" #> [4186] \"GeneID:151742\"    \"GeneID:84451\"     \"GeneID:7284\"      #> [4189] \"GeneID:100616275\" \"GeneID:2633\"      \"GeneID:260341\"    #> [4192] \"GeneID:100873990\" \"GeneID:79736\"     \"GeneID:3809\"      #> [4195] \"GeneID:246100\"    \"GeneID:5106\"      \"GeneID:2661\"      #> [4198] \"GeneID:101929406\" \"GeneID:2001\"      \"GeneID:4733\"      #> [4201] \"GeneID:100033425\" \"GeneID:1727\"      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\"GeneID:4897\"      #> [4942] \"GeneID:348761\"    \"GeneID:26749\"     \"GeneID:6585\"      #> [4945] \"GeneID:101930248\" \"GeneID:157983\"    \"GeneID:29844\"     #> [4948] \"GeneID:3976\"      \"GeneID:25920\"     \"GeneID:27079\"     #> [4951] \"GeneID:9658\"      \"GeneID:101927046\" \"GeneID:22980\"     #> [4954] \"GeneID:8939\"      \"GeneID:101929560\" \"GeneID:91289\"     #> [4957] \"GeneID:388730\"    \"GeneID:5451\"      \"GeneID:905\"       #> [4960] \"GeneID:9053\"      \"GeneID:25788\"     \"GeneID:101928349\" #> [4963] \"GeneID:91526\"     \"GeneID:83460\"     \"GeneID:26354\"     #> [4966] \"GeneID:693124\"    \"GeneID:101929352\" \"GeneID:5046\"      #> [4969] \"GeneID:101730217\" \"GeneID:102723306\" \"GeneID:100422957\" #> [4972] \"GeneID:728734\"    \"GeneID:91754\"     \"GeneID:83452\"     #> [4975] \"GeneID:26022\"     \"GeneID:1910\"      \"GeneID:8840\"      #> [4978] \"GeneID:101927614\" \"GeneID:440087\"    \"GeneID:4494\"      #> [4981] \"GeneID:100527950\" \"GeneID:101927873\" \"GeneID:388813\"    #> [4984] \"GeneID:3298\"      \"GeneID:100616211\" \"GeneID:3925\"      #> [4987] \"GeneID:114881\"    \"GeneID:9479\"      \"GeneID:100130733\" #> [4990] \"GeneID:58495\"     \"GeneID:100422971\" \"GeneID:8801\"      #> [4993] \"GeneID:101929951\" \"GeneID:101928474\" \"GeneID:285172\"    #> [4996] \"GeneID:54856\"     \"GeneID:26819\"     \"GeneID:101928992\" #> [4999] \"GeneID:79001\"     \"GeneID:79782\"     \"GeneID:100101115\" #> [5002] \"GeneID:100101116\" \"GeneID:100101117\" \"GeneID:100101118\" #> [5005] \"GeneID:100101120\" \"GeneID:100132596\" \"GeneID:100289087\" #> [5008] \"GeneID:100533178\" \"GeneID:100874056\" \"GeneID:101929148\" #> [5011] \"GeneID:102723934\" \"GeneID:114758\"    \"GeneID:114760\"    #> [5014] \"GeneID:114761\"    \"GeneID:140032\"    \"GeneID:159119\"    #> [5017] \"GeneID:159125\"    \"GeneID:159162\"    \"GeneID:159163\"    #> [5020] \"GeneID:1617\"      \"GeneID:203611\"    \"GeneID:22829\"     #> [5023] \"GeneID:246119\"    \"GeneID:246122\"    \"GeneID:246126\"    #> [5026] \"GeneID:252946\"    \"GeneID:252949\"    \"GeneID:252950\"    #> [5029] \"GeneID:252951\"    \"GeneID:252952\"    \"GeneID:252953\"    #> [5032] \"GeneID:252954\"    \"GeneID:252955\"    \"GeneID:253175\"    #> [5035] \"GeneID:286554\"    \"GeneID:286557\"    \"GeneID:340618\"    #> [5038] \"GeneID:353513\"    \"GeneID:353515\"    \"GeneID:378948\"    #> [5041] \"GeneID:378949\"    \"GeneID:401629\"    \"GeneID:401630\"    #> [5044] \"GeneID:425057\"    \"GeneID:441543\"    \"GeneID:442867\"    #> [5047] \"GeneID:442868\"    \"GeneID:474148\"    \"GeneID:474149\"    #> [5050] \"GeneID:474150\"    \"GeneID:474151\"    \"GeneID:50858\"     #> [5053] \"GeneID:5616\"      \"GeneID:57054\"     \"GeneID:57055\"     #> [5056] \"GeneID:57135\"     \"GeneID:5940\"      \"GeneID:60439\"     #> [5059] \"GeneID:6192\"      \"GeneID:64593\"     \"GeneID:6736\"      #> [5062] \"GeneID:7258\"      \"GeneID:728137\"    \"GeneID:728395\"    #> [5065] \"GeneID:728403\"    \"GeneID:7404\"      \"GeneID:7544\"      #> [5068] \"GeneID:8284\"      \"GeneID:83259\"     \"GeneID:83864\"     #> [5071] \"GeneID:83866\"     \"GeneID:83867\"     \"GeneID:83868\"     #> [5074] \"GeneID:83869\"     \"GeneID:84559\"     \"GeneID:84672\"     #> [5077] \"GeneID:84673\"     \"GeneID:8653\"      \"GeneID:86614\"     #> [5080] \"GeneID:90665\"     \"GeneID:9082\"      \"GeneID:9083\"      #> [5083] \"GeneID:9084\"      \"GeneID:9087\"      \"GeneID:9426\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_all_duplicated.html","id":null,"dir":"Reference","previous_headings":"","what":"Finding All Duplicates in Vector — h_all_duplicated","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"difference duplicated() also first occurrence duplicate flagged TRUE.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_all_duplicated.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"","code":"h_all_duplicated(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_all_duplicated.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"x vector data frame array NULL.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_all_duplicated.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"Logical vector flagging occurrences duplicate values TRUE.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_all_duplicated.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"","code":"h_all_duplicated(c(\"a\", \"a\", \"b\")) #> [1]  TRUE  TRUE FALSE duplicated(c(\"a\", \"a\", \"b\")) #> [1] FALSE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_df_factors_with_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"helper function converts character logical variables factor variables data.frame. also sets explicit missing data level factor variables least one NA. Empty strings handled NA.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_df_factors_with_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"","code":"h_df_factors_with_explicit_na(data, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_df_factors_with_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"data (data.frame) input data least one column. na_level (string) explicit missing level used.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_df_factors_with_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"modified data.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_df_factors_with_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"","code":"dat <- data.frame(   a = c(NA, 2),   b = c(\"A\", NA),   c = c(\"C\", \"D\"),   d = factor(c(NA, \"X\")),   e = factor(c(\"Y\", \"Z\")) ) h_df_factors_with_explicit_na(dat) #>    a         b c         d e #> 1 NA         A C <Missing> Y #> 2  2 <Missing> D         X Z"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":null,"dir":"Reference","previous_headings":"","what":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"helper functions performs differential expression analysis DESeq2::DESeq() given AnyHermesData input design matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"","code":"h_diff_expr_deseq2(object, design, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"object (HermesData) input. design (matrix) design matrix. ... additional arguments internally passed DESeq2::DESeq() (fitType, sfType, minReplicatesForReplace, useT, minmu).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"data frame columns log2_fc (estimated log2 fold change), stat (Wald statistic), p_val (raw p-value), adj_p_pval (Benjamini-Hochberg adjusted p-value).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"Love MI, Huber W, Anders S (2014). “Moderated estimation fold change dispersion RNA-seq data DESeq2.” Genome Biology, 15(12), 550. doi:10.1186/s13059-014-0550-8 .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_deseq2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"","code":"object <- hermes_data  # Create the design matrix corresponding to the factor of interest. design <- model.matrix(~SEX, colData(object))  # Then perform the `DESeq2` differential expression analysis. result <- h_diff_expr_deseq2(object, design) head(result) #>                 log2_fc      stat        p_val    adj_p_val #> GeneID:9834    5.859486  5.440035 5.327024e-08 0.0001852739 #> GeneID:221188  3.450713  4.805489 1.543734e-06 0.0026845539 #> GeneID:151242 -4.316426 -4.707534 2.507316e-06 0.0029068155 #> GeneID:9002    2.324969  4.390859 1.129039e-05 0.0097580091 #> GeneID:64344  -2.880611 -4.343419 1.402819e-05 0.0097580091 #> GeneID:4359    2.914210  4.206676 2.591542e-05 0.0113396717  # Change of the `fitType` can be required in some cases. result2 <- h_diff_expr_deseq2(object, design, fitType = \"local\") head(result2) #>                  log2_fc      stat        p_val    adj_p_val #> GeneID:9834    5.8595097  5.436419 5.436203e-08 0.0001605311 #> GeneID:221188  3.4507368  4.796226 1.616827e-06 0.0023872456 #> GeneID:151242 -4.3163441 -4.693049 2.691627e-06 0.0026494579 #> GeneID:9002    2.3249808  4.379230 1.190996e-05 0.0073970422 #> GeneID:64344  -2.8805945 -4.368250 1.252462e-05 0.0073970422 #> GeneID:51575  -0.7889652 -4.255997 2.081193e-05 0.0076822022"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":null,"dir":"Reference","previous_headings":"","what":"limma/voom Differential Expression Analysis — h_diff_expr_voom","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"helper functions performs differential expression analysis voom method limma package (via limma::voom(), limma::lmFit() limma::eBayes()) given counts AnyHermesData object corresponding design matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"","code":"h_diff_expr_voom(object, design, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"object (AnyHermesData) input. design (matrix) design matrix. ... additional arguments internally passed limma::eBayes() (robust, trend, proportion, winsor.tail.p, stdev.coef.lim).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"data frame columns log2_fc (estimated log2 fold change), stat (moderated t-statistic), p_val (raw p-value), adj_p_pval (Benjamini-Hochberg adjusted p-value).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"Ritchie , Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). “limma powers differential expression analyses RNA-sequencing microarray studies.” Nucleic Acids Research, 43(7), e47. doi:10.1093/nar/gkv007 . Law CW, Chen Y, Shi W, Smyth GK (2014). “voom: precision weights unlock linear model analysis tools RNA-seq read counts.” Genome Biology, 15(2), R29. doi:10.1186/gb-2014-15-2-r29 .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_diff_expr_voom.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"","code":"object <- hermes_data  # Create the design matrix corresponding to the factor of interest. design <- model.matrix(~SEX, colData(object))  # Then perform the differential expression analysis. result <- h_diff_expr_voom(object, design) head(result) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -4.239244 0.0004209192 0.9118348 #> GeneID:51227  -1.0467295 -4.032550 0.0006788432 0.9118348 #> GeneID:344558  1.6896266  3.824046 0.0010993677 0.9118348 #> GeneID:51575  -0.7760844 -3.746293 0.0013155805 0.9118348 #> GeneID:151242 -3.4358998 -3.570103 0.0019741997 0.9118348 #> GeneID:8904   -0.6100354 -3.542864 0.0021017199 0.9118348  # Sometimes we might want to specify method details. result2 <- h_diff_expr_voom(object, design, trend = TRUE, robust = TRUE) head(result2) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -3.848050 0.0008857274 0.8995289 #> GeneID:51227  -1.0467295 -3.724654 0.0011933484 0.8995289 #> GeneID:344558  1.6896266  3.684191 0.0013155791 0.8995289 #> GeneID:51575  -0.7760844 -3.498308 0.0020551283 0.8995289 #> GeneID:151242 -3.4358998 -3.441687 0.0023525055 0.8995289 #> GeneID:123036  2.9002547  3.431263 0.0024329189 0.8995289"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_ensembl_to_entrez_ids.html","id":null,"dir":"Reference","previous_headings":"","what":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"helper function queries BioMart translate Ensembl Entrez Gene IDs.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_ensembl_to_entrez_ids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"","code":"h_ensembl_to_entrez_ids(gene_ids, mart)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_ensembl_to_entrez_ids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"gene_ids (character)Ensembl gene IDs. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_ensembl_to_entrez_ids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"Character vector Entrez gene IDs.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_ensembl_to_entrez_ids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_ensembl_to_entrez_ids(c(\"ENSG00000135407\", \"ENSG00000241644\"), mart) }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_annotation_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotations from BioMart — h_get_annotation_biomart","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"Helper function query annotations biomaRt, cleaned gene IDs specific ID variable given biomaRt::Mart.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_annotation_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"","code":"h_get_annotation_biomart(gene_ids, id_var, mart)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_annotation_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"gene_ids (character) gene IDs, e.g. 10329, .e. already without Entrez GeneID prefix, ENSG00000241644 Ensembl gene ID. id_var (string) corresponding gene ID variable name BioMart, .e. entrezgene_id ensembl_gene_id. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_annotation_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"data frame columns: id_var (depending used) hgnc_symbol entrezgene_description chromosome_name size refseq_mrna refseq_peptide","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_annotation_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_get_annotation_biomart(c(\"11185\", \"10677\"), id_var = \"entrezgene_id\", mart = mart) }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_granges_by_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"function extracts chromosome number, start position end position transcripts given data.frame coordinates returned biomaRt::getBM() converts GRanges object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_granges_by_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"","code":"h_get_granges_by_id(coords, id)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_granges_by_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"coords (data.frame) returned biomaRt::getBM(), containing columns ensembl_gene_id, chromosome_name, exon_chrom_start, exon_chrom_end. id (string) single Ensembl gene ID convert coordinates .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_granges_by_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"GRange objects respective single gene ID.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_granges_by_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   attrs <- c(     \"ensembl_gene_id\",     \"ensembl_exon_id\",     \"chromosome_name\",     \"exon_chrom_start\",     \"exon_chrom_end\"   )   coords <- biomaRt::getBM(     filters = \"entrezgene_id\",     attributes = attrs,     values = c(\"11185\", \"10677\"),     mart = mart   )   h_get_granges_by_id(coords, \"ENSG00000135407\") }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_size_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Total Length of All Exons for Genes — h_get_size_biomart","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"helper function queries BioMart lengths genes adding exon lengths reducing overlaps.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_size_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"","code":"h_get_size_biomart(gene_ids, id_var, mart)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_size_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"gene_ids (character) gene IDs, e.g. 10329, .e. already without Entrez GeneID prefix, ENSG00000241644 Ensembl gene ID. id_var (string) corresponding gene ID variable name BioMart, .e. entrezgene_id ensembl_gene_id. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_size_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"Named integer vector indicating gene lengths.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_get_size_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_get_size_biomart(\"11185\", \"entrezgene_id\", mart)   h_get_size_biomart(\"ENSG00000215417\", \"ensembl_gene_id\", mart)   h_get_size_biomart(c(\"11185\", \"10677\"), \"entrezgene_id\", mart)   h_get_size_biomart(c(\"ENSG00000135407\", \"ENSG00000215417\"), \"ensembl_gene_id\", mart) }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_has_req_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Predicate for Required Annotations — h_has_req_annotations","title":"Predicate for Required Annotations — h_has_req_annotations","text":"helper function determines gene object whether required annotation columns filled.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_has_req_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predicate for Required Annotations — h_has_req_annotations","text":"","code":"h_has_req_annotations(object, annotation_required)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_has_req_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predicate for Required Annotations — h_has_req_annotations","text":"object (AnyHermesData) input object. annotation_required (character) names required annotation columns genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_has_req_annotations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predicate for Required Annotations — h_has_req_annotations","text":"Named logical vector one value gene object, TRUE required annotation columns filled, otherwise FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_has_req_annotations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Predicate for Required Annotations — h_has_req_annotations","text":"","code":"object <- hermes_data result <- h_has_req_annotations(object, \"size\") all(result) #> [1] TRUE rowData(object)$size[1] <- NA # nolint which(!h_has_req_annotations(object, \"size\")) #> GeneID:11185  #>            1"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_map_pos.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Matching Map Values to Names — h_map_pos","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"used rename method. wraps assertions matching used several times.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_map_pos.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"","code":"h_map_pos(names, map)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_map_pos.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"names (character) original names. map (named character) mapping vector old (value) new (name) names. values must included names.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_map_pos.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"Integer vector positions map values names.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_map_pos.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"","code":"h_map_pos(c(\"a\", \"b\"), c(d = \"b\")) #> [1] 2"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_parens.html","id":null,"dir":"Reference","previous_headings":"","what":"Parenthesize a Character Vector — h_parens","title":"Parenthesize a Character Vector — h_parens","text":"helper function adds parentheses around element character vector.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_parens.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parenthesize a Character Vector — h_parens","text":"","code":"h_parens(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_parens.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parenthesize a Character Vector — h_parens","text":"x (character) inputs parenthesized.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_parens.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parenthesize a Character Vector — h_parens","text":"Character vector parentheses, except x blank string case returned unaltered.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_parens.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parenthesize a Character Vector — h_parens","text":"","code":"h_parens(\"bla\") #> [1] \"(bla)\" h_parens(\"\") #> [1] \"\" h_parens(c(\"bla\", \"bli\")) #> [1] \"(bla)\" \"(bli)\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"function processes sample variables AnyHermesData corresponding principal components matrix, generates matrix R2 values.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"","code":"h_pca_df_r2_matrix(pca, df)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"pca (matrix) comprises principal components generated calc_pca(). df (data.frame) SummarizedExperiment::colData() AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"matrix R2 values combinations sample variables principal components.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"Note df columns numeric, character, factor logical included resulting matrix, variable types supported. addition, df columns constant, NA, character factor columns many levels also dropped analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_df_r2_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Obtain the principal components. pca <- calc_pca(object)$x  # Obtain the `colData` as a `data.frame`. df <- as.data.frame(colData(object))  # Correlate them. r2_all <- h_pca_df_r2_matrix(pca, df) str(r2_all) #>  num [1:18, 1:39] 0.102 0.183 0.147 0.391 0.662 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:18] \"PC1\" \"PC2\" \"PC3\" \"PC4\" ... #>   ..$ : chr [1:39] \"AGEGRP\" \"AGE18\" \"STDDRS\" \"STDDRSD\" ...  # We can see that only about half of the columns from `df` were # used for the correlations. ncol(r2_all) #> [1] 39 ncol(df) #> [1] 74"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"helper function calculates R2 values one sample variable AnyHermesData Principal Components (PCs) separately (one linear model fit PC).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"","code":"h_pca_var_rsquared(pca, x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"pca (matrix) principal components matrix generated calc_pca(). x (vector) values one sample variable AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"vector R2 values principal component.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"Note case estimation problems PCs, NA returned .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_pca_var_rsquared.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Obtain the principal components. pca <- calc_pca(object)$x  # Obtain the sample variable. x <- colData(object)$AGE18  # Correlate them. r2 <- h_pca_var_rsquared(pca, x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_short_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a Short List of a Character Vector — h_short_list","title":"Make a Short List of a Character Vector — h_short_list","text":"helper function makes short list string, e.g. \", b, ..., z\" character vector, e.g. letters.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_short_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a Short List of a Character Vector — h_short_list","text":"","code":"h_short_list(x, sep = \", \", thresh = 3L)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_short_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a Short List of a Character Vector — h_short_list","text":"x (character) input listed. sep (string) separator use. thresh (count) threshold use, length x larger list shortened using ... ellipsis.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_short_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a Short List of a Character Vector — h_short_list","text":"String short list.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_short_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make a Short List of a Character Vector — h_short_list","text":"","code":"h_short_list(letters) #> [1] \"a, b, ..., z\" h_short_list(letters[1:3]) #> [1] \"a, b, c\" h_short_list(LETTERS[1:5], sep = \";\", thresh = 5L) #> [1] \"A;B;C;D;E\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":null,"dir":"Reference","previous_headings":"","what":"Stripping Prefix from Gene IDs — h_strip_prefix","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"helper function removes prefix possible delimiter vector gene IDs, digits returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"","code":"h_strip_prefix(gene_ids, prefix)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"gene_ids (character) original gene IDs including prefix optional delimiter digits. prefix (string) common prefix stripped away gene_ids.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"Character vector contains digits gene ID.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"currently used strip away GeneID prefix Entrez gene IDs can queried BioMart","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_strip_prefix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"","code":"h_strip_prefix(c(\"GeneID:11185\", \"GeneID:10677\"), prefix = \"GeneID\") #> [1] \"11185\" \"10677\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_unique_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Creation of Unique Labels — h_unique_labels","title":"Creation of Unique Labels — h_unique_labels","text":"helper function generates set unique labels given unique IDs necessarily unique names.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_unique_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creation of Unique Labels — h_unique_labels","text":"","code":"h_unique_labels(ids, nms = NULL)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_unique_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creation of Unique Labels — h_unique_labels","text":"ids (character NULL) unique IDs. nms (character NULL) necessarily unique names provided.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_unique_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creation of Unique Labels — h_unique_labels","text":"Character vector empty names replaced IDs non-unique names made unique appending IDs parentheses.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/h_unique_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creation of Unique Labels — h_unique_labels","text":"","code":"h_unique_labels(c(\"1\", \"2\", \"3\"), c(\"A\", \"B\", \"A\")) #> [1] \"A (1)\" \"B\"     \"A (3)\" h_unique_labels(NULL) #> NULL h_unique_labels(c(\"1\", \"2\", \"3\")) #> [1] \"1\" \"2\" \"3\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"hermes Package — hermes-package","title":"hermes Package — hermes-package","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"hermes Package — hermes-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@rconis.com Authors: Namrata Bhatia Stefanie Bienert Benoit Falquet Haocheng Li Jeff Luong Lyndsee Midori Zhang zhang.lyndsee@gene.com Alex Richardson Simona Rossomanno Tim Treis Mark Yan Naomi Chang Chendi Liao chendi.liao@roche.com Carolyn Zhang Joseph N. Paulson paulson.joseph@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Example HermesData Data — hermes_data","title":"Example HermesData Data — hermes_data","text":"example HermesData created underlying SummarizedExperiment::SummarizedExperiment object renaming descriptors align standard specification. already contains required columns rowData colData.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example HermesData Data — hermes_data","text":"","code":"hermes_data"},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example HermesData Data — hermes_data","text":"HermesData object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/hermes_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example HermesData Data — hermes_data","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"useful function trying join genetic CDISC data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"","code":"inner_join_cdisc(   gene_data,   cdisc_data,   patient_key = \"USUBJID\",   additional_keys = character() )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"gene_data (data.frame DataFrame) genetic data. cdisc_data (data.frame) CDISC data (typically patient level data). patient_key (string) patient identifier. additional_keys (character) potential additional keys two data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"data.frame contains columns data sets merged keys.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"Columns contained data sets specified keys taken gene_data cdisc_data.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/inner_join_cdisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"","code":"gene_data <- col_data_with_genes(hermes_data, \"counts\", gene_spec(\"GeneID:1820\")) cdisc_data <- data.frame(   USUBJID = head(gene_data$USUBJID, 10),   extra = 1:10 ) result <- inner_join_cdisc(gene_data, cdisc_data) #> Warning: Patients AB12345-CHN-7-id-28, AB12345-CHN-4-id-73, AB12345-RUS-1-id-52, AB12345-PAK-11-id-268, AB12345-CHN-13-id-102, AB12345-CHN-17-id-84, AB12345-BRA-11-id-9, AB12345-CHN-4-id-115, AB12345-CHN-15-id-245, AB12345-CHN-4-id-370 from gene data set were lost because they could not be joined to CDISC data set result #>                  USUBJID Filename       SampleID         AGEGRP AGE18 STDDRS #> 1   AB12345-CHN-1-id-307     eset 06520046C0018R 12 - <18 years  < 18  DEATH #> 2  AB12345-CHN-11-id-220     eset 06520105C0017R 12 - <18 years  < 18        #> 3  AB12345-CHN-15-id-201     eset 06520103C0017R    >= 18 years >= 18  DEATH #> 4  AB12345-CHN-15-id-262     eset 06520067C0018R   2 - <6 years  < 18        #> 5   AB12345-CHN-3-id-128     eset 06520011B0023R    >= 18 years >= 18  DEATH #> 6   AB12345-CHN-7-id-267     eset 06520092C0017R 12 - <18 years  < 18  DEATH #> 7  AB12345-NGA-11-id-173     eset 06520062C0017R  6 - <12 years  < 18  DEATH #> 8   AB12345-RUS-3-id-378     eset 06520063C0043R 12 - <18 years  < 18  DEATH #> 9   AB12345-USA-1-id-261     eset 06520022C0017R 12 - <18 years  < 18        #> 10   AB12345-USA-1-id-45     eset 06520001B0023R    >= 18 years >= 18  DEATH #>                                STDDRSD    STDSSDT              TRTDRS #> 1  DEATH DUE TO PROGRESSION OF DISEASE 07/24/2016 PROGRESSIVE DISEASE #> 2                                                 PROGRESSIVE DISEASE #> 3  DEATH DUE TO PROGRESSION OF DISEASE 08/12/2016 PROGRESSIVE DISEASE #> 4                                                 PROGRESSIVE DISEASE #> 5  DEATH DUE TO PROGRESSION OF DISEASE 05/31/2016       ADVERSE EVENT #> 6  DEATH DUE TO PROGRESSION OF DISEASE 02/16/2017 PROGRESSIVE DISEASE #> 7  DEATH DUE TO PROGRESSION OF DISEASE 09/11/2016 PROGRESSIVE DISEASE #> 8  DEATH DUE TO PROGRESSION OF DISEASE 08/05/2016 PROGRESSIVE DISEASE #> 9                                                 PROGRESSIVE DISEASE #> 10 DEATH DUE TO PROGRESSION OF DISEASE 01/08/2016 PROGRESSIVE DISEASE #>                   TRTDRSD BHDCIRC BHDCIRCU ADAFL BLANP BKPS BLKS BTANNER #> 1  PROGRESSION OF DISEASE      NA              Y    NA   80   80      NA #> 2  PROGRESSION OF DISEASE      NA              Y   100   NA  100      NA #> 3  PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #> 4  PROGRESSION OF DISEASE      NA              Y    NA  100  100      NA #> 5           ADVERSE EVENT      NA              Y   100   NA  100      NA #> 6  PROGRESSION OF DISEASE      NA              Y   100   NA  100      NA #> 7  PROGRESSION OF DISEASE      NA              Y    NA  100  100      NA #> 8  PROGRESSION OF DISEASE      NA              Y    90   NA   90      NA #> 9  PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #> 10 PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #>             FRPST     DURIDX    DURSAF    DURSUR LNTHRPY AENCIFL STUDYID #> 1  POST-MENARCHAL  61.667351 1.6755647  5.158111       5      NA AB12345 #> 2   PRE-MENARCHAL  14.981520 3.0882957  5.815195       4      NA AB12345 #> 3                  10.841889 0.9856263  3.055441       4      NA AB12345 #> 4                 131.088296 1.6755647 19.252567       3      NA AB12345 #> 5                  55.030801 0.9856263  5.026694       3      NA AB12345 #> 6                   7.687885 3.0225873 12.418891       1      NA AB12345 #> 7                  99.285421 3.5811088  6.340862       7      NA AB12345 #> 8                  93.568789 0.9856263  4.665298       3      NA AB12345 #> 9                  41.626283 1.6755647 18.858316       3      NA AB12345 #> 10                 45.733060 0.6570842  2.299795       2      NA AB12345 #>             RFSTDTC          RFENDTC         RFXSTDTC         RFXENDTC #> 1  2016-03-10T14:05 2016-03-31T15:49 2016-03-10T14:05 2016-03-31T15:49 #> 2  2017-04-11T12:35 2017-06-14T11:45 2017-04-11T12:35 2017-06-14T11:45 #> 3  2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10 #> 4  2016-01-11T14:30 2016-02-01T13:30 2016-01-11T14:30 2016-02-01T13:30 #> 5  2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37 #> 6  2016-02-12T11:05 2016-04-14T12:00 2016-02-12T11:05 2016-04-14T12:00 #> 7  2016-03-21T15:40 2016-06-08T18:00 2016-03-21T15:40 2016-06-08T18:00 #> 8  2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25 #> 9  2016-02-08T12:37 2016-02-29T14:15 2016-02-08T12:37 2016-02-29T14:15 #> 10 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00 #>       RFICDTC   RFPENDTC     DTHDTC DTHFL SITEID  INVID AGE  AGEU SEX #> 1  2016-02-18 2016-07-24 2016-07-24     Y 283495 223804  12 YEARS   F #> 2  2017-04-03                             283694 456732  15 YEARS   M #> 3  2016-05-11 2016-08-12 2016-08-12     Y 282087 468105  27 YEARS   F #> 4  2016-01-07                             282087 468105   2 YEARS   F #> 5  2015-12-30 2016-05-31 2016-05-31     Y 283495 223804  19 YEARS   F #> 6  2016-02-04 2017-02-16 2017-02-16     Y 280959  20842  16 YEARS   M #> 7  2016-03-02 2016-09-11 2016-09-11     Y 283497 241874   7 YEARS   F #> 8  2016-03-16 2016-08-05 2016-08-05     Y 284024 457432  13 YEARS   M #> 9  2016-02-01                             281049 457179  16 YEARS   F #> 10 2015-10-30 2016-01-08 2016-01-08     Y 283971 235545  19 YEARS   F #>                         RACE                 ETHNIC ARMCD       ARM ACTARMCD #> 1                      WHITE NOT HISPANIC OR LATINO  COH3  COHORT 3     COH3 #> 2                      WHITE NOT HISPANIC OR LATINO COH12 COHORT 12    COH12 #> 3                    UNKNOWN           NOT REPORTED COH9E COHORT 9E    COH9E #> 4                    UNKNOWN           NOT REPORTED  COH1  COHORT 1     COH1 #> 5                   MULTIPLE NOT HISPANIC OR LATINO  COH1  COHORT 1     COH1 #> 6                      WHITE NOT HISPANIC OR LATINO COH9O COHORT 9O    COH9O #> 7  BLACK OR AFRICAN AMERICAN     HISPANIC OR LATINO  COH6  COHORT 6     COH6 #> 8                      WHITE NOT HISPANIC OR LATINO  COH8  COHORT 8     COH8 #> 9                      ASIAN NOT HISPANIC OR LATINO  COH1  COHORT 1     COH1 #> 10                   UNKNOWN     HISPANIC OR LATINO  COH6  COHORT 6     COH6 #>       ACTARM COUNTRY      DMDTC DMDY BAGE BAGEU    BWT BWTU   BHT BHTU     BBMI #> 1   COHORT 3     CHN 2016-02-18  -21   12 YEARS  50.00   kg 157.0   cm 20.28480 #> 2  COHORT 12     CHN 2017-04-04   -7   15 YEARS  26.15   kg 136.0   cm 14.13819 #> 3   COHORT 9     CHN 2016-05-25   -6   27 YEARS  61.60   kg 173.0   cm 20.58204 #> 4   COHORT 1     CHN 2016-01-07   -4    2 YEARS  64.60   kg 177.1   cm 20.59659 #> 5   COHORT 1     CHN 2015-12-30  -15   19 YEARS  40.60   kg 154.0   cm 17.11924 #> 6   COHORT 9     CHN 2016-02-04   -8   16 YEARS  45.20   kg 161.1   cm 17.41596 #> 7   COHORT 6     NGA 2016-03-02  -19    7 YEARS  53.90   kg 176.0   cm 17.40057 #> 8   COHORT 8     RUS 2016-03-22   -2   13 YEARS  25.40   kg 125.0   cm 16.25600 #> 9   COHORT 1     USA 2016-02-01   -7   16 YEARS 104.70   kg 172.0   cm 35.39075 #> 10  COHORT 6     USA 2015-10-30   -6   19 YEARS  57.00   kg 172.0   cm 19.26717 #>    ITTFL SAFFL    INFCODT     RANDDT          TRTSDTC             TRTSDTM #> 1      Y     Y 2016-02-18 2016-03-09 2016-03-10T14:05 2016-03-10 14:05:00 #> 2      Y     Y 2017-04-03 2017-04-11 2017-04-11T12:35 2017-04-11 12:35:00 #> 3      Y     Y 2016-05-11 2016-05-31 2016-05-31T14:10 2016-05-31 14:10:00 #> 4      Y     Y 2016-01-07 2016-01-11 2016-01-11T14:30 2016-01-11 14:30:00 #> 5      Y     Y 2015-12-30 2016-01-14 2016-01-14T12:37 2016-01-14 12:37:00 #> 6      Y     Y 2016-02-04 2016-02-09 2016-02-12T11:05 2016-02-12 11:05:00 #> 7      Y     Y 2016-03-02 2016-03-21 2016-03-21T15:40 2016-03-21 15:40:00 #> 8      Y     Y 2016-03-16 2016-03-24 2016-03-24T14:25 2016-03-24 14:25:00 #> 9      Y     Y 2016-02-01 2016-02-03 2016-02-08T12:37 2016-02-08 12:37:00 #> 10     Y     Y 2015-10-30 2015-11-05 2015-11-05T11:00 2015-11-05 11:00:00 #>    TRTSTMF             TRTEDTM TRTETMF TRTDUR DISCSTUD DISCDEAT DISCAE DISTRTFL #> 1        S 2016-03-31 16:55:59       S     22        Y        Y      N        Y #> 2        S 2017-06-14 12:15:59       S     65        N        N      N        Y #> 3        S 2016-05-31 15:10:59       S      1        Y        Y      N        Y #> 4        S 2016-02-01 14:30:59       S     22        N        N      N        Y #> 5        S 2016-01-14 13:37:59       S      1        Y        Y      N        Y #> 6        S 2016-04-14 12:30:59       S     63        Y        Y      N        Y #> 7        S 2016-06-08 18:30:59       S     80        Y        Y      N        Y #> 8        S 2016-03-24 15:30:59       S      1        Y        Y      N        Y #> 9        S 2016-02-29 14:48:59       S     22        N        N      N        Y #> 10       S 2015-11-05 12:00:59       S      1        Y        Y      N        Y #>    AEWITHFL     ALIVDT #> 1         N 2016-07-24 #> 2         N 2017-09-27 #> 3         N 2016-08-12 #> 4         N 2017-08-15 #> 5         Y 2016-05-31 #> 6         N 2017-02-16 #> 7         N 2016-09-11 #> 8         N 2016-08-05 #> 9         N 2017-08-28 #> 10        N 2016-01-08 #>                                                           COHORT #> 1                                       Cohort 3 (NEUROBLASTOMA) #> 2                    Cohort 12 (ATYPICAL TERATOID RHABOID TUMOR) #> 3  Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION) #> 4                                       Cohort 1 (EWING SARCOMA) #> 5                                       Cohort 1 (EWING SARCOMA) #> 6  Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION) #> 7                                        Cohort 6 (OSTEOSARCOMA) #> 8                                         Cohort 8 (WILMS TUMOR) #> 9                                       Cohort 1 (EWING SARCOMA) #> 10                                       Cohort 6 (OSTEOSARCOMA) #>                                                                                                                                        TTYPE #> 1                                                                                                                              NEUROBLASTOMA #> 2                                                                                                           ATYPICAL TERATOID RHABDOID TUMOR #> 3                                                 GERM CELL TUMOR - YOLK SAC TUMOR (ENDODERMAL SINUS TUMOR) WITH DOCUMENTED PD-L1 EXPRESSION #> 4                                                                                                                              EWING SARCOMA #> 5                                                                                                                              EWING SARCOMA #> 6  OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION ON EITHER TUMOR CELLS OR IMMUNE CELLS (TUMORS TYPE MUST NOT BE INCLUDED IN LIST ABOVE) #> 7                                                                                                                               OSTEOSARCOMA #> 8                                                                                                                                WILMS TUMOR #> 9                                                                                                                              EWING SARCOMA #> 10                                                                                                                              OSTEOSARCOMA #>    STDSSDY low_depth_flag tech_failure_flag GeneID.1820 extra #> 1      137          FALSE             FALSE          16    10 #> 2       NA          FALSE             FALSE          54     4 #> 3       74          FALSE             FALSE         567     6 #> 4       NA          FALSE             FALSE         153     2 #> 5      139          FALSE             FALSE          49     1 #> 6      371          FALSE             FALSE         111     5 #> 7      175           TRUE             FALSE         180     9 #> 8      135           TRUE             FALSE          94     3 #> 9       NA          FALSE             FALSE         171     8 #> 10      65          FALSE             FALSE         118     7"},{"path":"https://insightsengineering.github.io/hermes/main/reference/isEmpty.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"method checks whether SummarizedExperiment::SummarizedExperiment object empty.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/isEmpty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"","code":"# S4 method for SummarizedExperiment isEmpty(x)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/isEmpty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"x (SummarizedExperiment) object check.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/isEmpty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"Flag whether object empty.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/isEmpty.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"","code":"isEmpty(summarized_experiment) #> [1] FALSE isEmpty(summarized_experiment[NULL, ]) #> [1] TRUE isEmpty(hermes_data) #> [1] FALSE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/lapply.html","id":null,"dir":"Reference","previous_headings":"","what":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"Apply function experiments MAE.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/lapply.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"","code":"# S4 method for MultiAssayExperiment lapply(X, FUN, safe = TRUE, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/lapply.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"X (MultiAssayExperiment) input. FUN (function) applied experiment X. safe (flag) whether method skip experiments function fails. ... additional arguments passed FUN.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/lapply.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"MultiAssayExperiment object specified function applied.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/lapply.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"","code":"object <- multi_assay_experiment result <- lapply(object, normalize, safe = TRUE) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. # Similarly, all experiments in an MAE can be converted to HermesData class: result <- lapply(object, HermesData, safe = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata Accessor and Setter — metadata","title":"Metadata Accessor and Setter — metadata","text":"methods access set metadata AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata Accessor and Setter — metadata","text":"x (AnyHermesData) object access metadata . value (list) list replace current metadata .","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata Accessor and Setter — metadata","text":"metadata list.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/metadata.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Metadata Accessor and Setter — metadata","text":"Note just inherits S4Vectors::metadata,Annotated-method().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata Accessor and Setter — metadata","text":"","code":"a <- hermes_data metadata(a) #> list() metadata(a) <- list(new = \"my metadata\") metadata(a) #> $new #> [1] \"my metadata\" #>"},{"path":"https://insightsengineering.github.io/hermes/main/reference/multi_assay_experiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Example MultiAssayExperiment Data — multi_assay_experiment","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"example MultiAssayExperiment::MultiAssayExperiment can used test data.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/multi_assay_experiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"","code":"multi_assay_experiment"},{"path":"https://insightsengineering.github.io/hermes/main/reference/multi_assay_experiment.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"MultiAssayExperiment::MultiAssayExperiment object 3 separate HermesData objects. first object contains 5 samples covers 1000 features (Entrez gene IDs). second object contains 9 samples 2500 features. third object contains 6 samples 1300 features.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/multi_assay_experiment.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"artificial dataset designed resemble real data.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"normalize() method normalizing input AnyHermesData according one specified normalization methods. results saved additional assays object. Possible normalization methods (implemented separate helper functions): cpm: Counts per Million (CPM). Separately sample, original counts genes divided library size sample, multiplied one million. appropriate normalization -sample comparisons. rpkm: Reads per Kilobase transcript per Million reads mapped (RPKM). gene count divided gene size (kilobases) divided library sizes sample (millions). allows within-sample comparisons, takes account gene sizes - longer genes always counts shorter genes. tpm: Transcripts per Million (TPM). addresses problem RPKM inconsistent across samples (can seen sum RPKM values vary sample sample). Therefore divide RPKM sum RPKM values sample, multiply one million. voom: VOOM normalization. essentially just slight variation CPM prior_count 0.5 combined lib_sizes increased 1 sample. Note required corresponding differential expression analysis, just provided complementary experimental normalization approach . vst: Variance stabilizing transformation. transform normalized count data genes approximately homoskedastic values (constant variance). rlog: transformation log2 scale values approximately homoskedastic values.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData normalize(   object,   methods = c(\"cpm\", \"rpkm\", \"tpm\", \"voom\", \"vst\"),   control = control_normalize(),   ... )  h_cpm(object, control = control_normalize())  h_rpkm(object, control = control_normalize())  h_tpm(object, control = control_normalize())  h_voom(object, control = control_normalize())  h_vst(object, control = control_normalize())  h_rlog(object, control = control_normalize())"},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"object (AnyHermesData) object normalize. methods (character) normalization methods use, see details. control (named list) settings produced control_normalize(). ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"AnyHermesData object additional assays containing normalized counts. control saved metadata object future reference.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"h_cpm(): calculates Counts per Million (CPM) normalized counts. h_rpkm(): calculates Reads per Kilobase per Million (RPKM) normalized counts. h_tpm(): calculates Transcripts per Million (TPM) normalized counts. h_voom(): calculates VOOM normalized counts. h_vst(): variance stabilizing transformation (vst) DESeq2 package. h_rlog(): regularized log transformation (rlog) DESeq2 package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"","code":"a <- hermes_data  # By default, log values are used with a prior count of 1 added to original counts. result <- normalize(a) assayNames(result) #> [1] \"counts\" \"cpm\"    \"rpkm\"   \"tpm\"    \"voom\"   \"vst\"    tpm <- assay(result, \"tpm\") tpm[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185          0.8626554       3.993877       3.591742 #> GeneID:10677          7.0670966       4.054655       3.289554 #> GeneID:101928428      0.0000000       0.000000       0.000000  # We can also work on original scale. result_orig <- normalize(a, control = control_normalize(log = FALSE)) tpm_orig <- assay(result_orig, \"tpm\") tpm_orig[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185          0.8183821       14.93224       11.05653 #> GeneID:10677        133.0936048       15.61778        8.77810 #> GeneID:101928428      0.0000000        0.00000        0.00000  # Separate calculation of the CPM normalized counts. counts_cpm <- h_cpm(a) str(counts_cpm) #>  num [1:5085, 1:20] -0.453 8.252 -2.453 -2.453 -2.453 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the RPKM normalized counts. counts_rpkm <- h_rpkm(a) str(counts_rpkm) #>  num [1:5085, 1:20] -2.904 4.027 0.404 1.12 1.323 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the TPM normalized counts. counts_tpm <- h_tpm(a) str(counts_tpm) #>  num [1:5085, 1:20] 0.863 7.067 0 0 0 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the VOOM normalized counts. counts_voom <- h_voom(a) str(counts_voom) #>  num [1:5085, 1:20] -0.645 8.251 -3.453 -3.453 -3.453 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the vst transformation. counts_vst <- h_vst(a) str(counts_vst) #>  num [1:5085, 1:20] 3.03 10.6 1.78 1.78 1.78 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the rlog transformation. counts_rlog <- h_rlog(a) str(counts_rlog) #>  num [1:5085, 1:20] 2.97 10.13 0 0 0 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ... #>  - attr(*, \"betaPriorVar\")= num 7.01 #>  - attr(*, \"intercept\")= num [1:5085, 1] 5.26 8.49 -Inf -Inf -Inf ..."},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"correlate() method analyses correlations (R2 values) sample variables AnyHermesData object principal components samples. corresponding autoplot() method can visualize results heatmap.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"","code":"# S4 method for HermesDataPca correlate(object, data)  # S4 method for HermesDataPcaCor autoplot(   object,   cor_colors = circlize::colorRamp2(c(-1, 0, 1), c(\"blue\", \"white\", \"red\")),   ... )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"object (HermesDataPca) input. can generated using calc_pca() function AnyHermesData. data (AnyHermesData) input used originally PCA. cor_colors (function) color scale function correlation values heatmap, produced circlize::colorRamp2(). ... arguments passed ComplexHeatmap::Heatmap().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"HermesDataPcaCor object R2 values sample variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"autoplot(HermesDataPcaCor): plot method uses ComplexHeatmap::Heatmap() function visualize HermesDataPcaCor object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/pca_cor_samplevar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Perform PCA and then correlate the prinicipal components with the sample variables. object_pca <- calc_pca(object) result <- correlate(object_pca, object)  # Visualize the correlations in a heatmap. autoplot(result)   # We can also choose to not reorder the columns. autoplot(result, cluster_columns = FALSE)   # We can also choose break-points for color customization. autoplot(   result,   cor_colors = circlize::colorRamp2(     c(-0.5, -0.25, 0, 0.25, 0.5, 0.75, 1),     c(\"blue\", \"green\", \"purple\", \"yellow\", \"orange\", \"red\", \"brown\")   ) )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://insightsengineering.github.io/hermes/main/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result corresponding function call.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/pipe.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pipe operator — %>%","text":"","code":"hermes_data %>%   filter() %>%   normalize() %>%   summary() #> HermesData object with 18 samples of 2064 genes. #> - Library sizes across samples: mean 1997557, median 2007086, range 1595589 to 2374075 #> - Included assays (6): counts cpm ... voom vst #> - Additional gene information (3): GeneID SYMBOL chromosome_name #> - Additional sample information (72): Filename SampleID ... TTYPE #>   STDSSDY #> - Low expression genes (0): #> - Samples with too low depth or technical failures (0):"},{"path":"https://insightsengineering.github.io/hermes/main/reference/plot_all.html","id":null,"dir":"Reference","previous_headings":"","what":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"generates standard plots - histogram q-q plot library sizes, density plot (log) counts distributions, boxplot number number non-zero expressed genes per sample, stacked barplot low expression genes chromosome default setting.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/plot_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData autoplot(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/plot_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/plot_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"list ggplot objects draw_libsize_hist(), draw_libsize_qq(), draw_libsize_densities(), draw_nonzero_boxplot() draw_genes_barplot() functions default settings.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/plot_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"","code":"result <- hermes_data autoplot(result)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/prefix.html","id":null,"dir":"Reference","previous_headings":"","what":"Prefix Accessor — prefix","title":"Prefix Accessor — prefix","text":"Generic function access prefix object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/prefix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prefix Accessor — prefix","text":"","code":"prefix(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/prefix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prefix Accessor — prefix","text":"object (AnyHermesData) input. ... additional arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/prefix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prefix Accessor — prefix","text":"prefix slot contents.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/prefix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prefix Accessor — prefix","text":"","code":"a <- hermes_data prefix(a) #> [1] \"GeneID\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Quality Flags — add_quality_flags","title":"Add Quality Flags — add_quality_flags","text":"function add_quality_flags() adds quality flag information AnyHermesData object: low_expression_flag: gene, counts many samples pass minimum expression Counts per Million (CPM) threshold. many, flags gene \"low expression\" gene. tech_failure_flag: first calculates Pearson correlation matrix sample wise CPM values, resulting matrix measuring correlation samples. compares average correlation per sample threshold - low, sample flagged \"technical failure\" sample. low_depth_flag: computes library size (total number counts) per sample. number low, sample flagged \"low depth\" sample. Separate helper functions internally used create flags, separate getter functions allow easy access quality control flags object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Quality Flags — add_quality_flags","text":"","code":"add_quality_flags(object, control = control_quality(), overwrite = FALSE)  h_low_expression_flag(object, control = control_quality())  h_low_depth_flag(object, control = control_quality())  h_tech_failure_flag(object, control = control_quality())  get_tech_failure(object)  get_low_depth(object)  get_low_expression(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Quality Flags — add_quality_flags","text":"object (AnyHermesData)  input. control (list)  list settings (thresholds etc.) used compute quality control flags, produced control_quality(). overwrite (flag) whether previously added flags may overwritten.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Quality Flags — add_quality_flags","text":"input object added quality flags.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Quality Flags — add_quality_flags","text":"object already variables mentioned part rowData colData (enforced validation method AnyHermesData), usually still NA initial object creation.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Add Quality Flags — add_quality_flags","text":"h_low_expression_flag(): creates low expression flag genes given control settings. h_low_depth_flag(): creates low depth (library size) flag samples given control settings. h_tech_failure_flag(): creates technical failure flag samples given control settings. get_tech_failure(): get technical failure flags samples. get_low_depth(): get low depth failure flags samples. get_low_expression(): get low expression failure flags genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/quality_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Quality Flags — add_quality_flags","text":"","code":"# Adding default quality flags to `AnyHermesData` object. object <- hermes_data result <- add_quality_flags(object) which(get_tech_failure(result) != get_tech_failure(object)) #> 06520046C0018R  #>             10  head(get_low_expression(result)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>            FALSE            FALSE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE  head(get_tech_failure(result)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_depth(result)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE   # It is possible to overwrite flags if needed, which will trigger a message. result2 <- add_quality_flags(result, control_quality(min_cpm = 1000), overwrite = TRUE) #> previously have added quality flags, but overwriting now  # Separate calculation of low expression flag. low_expr_flag <- h_low_expression_flag(   object,   control_quality(min_cpm = 500, min_cpm_prop = 0.9) ) length(low_expr_flag) == nrow(object) #> [1] TRUE head(low_expr_flag) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>             TRUE             TRUE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE   # Separate calculation of low depth flag. low_depth_flag <- h_low_depth_flag(object, control_quality(min_depth = 5)) length(low_depth_flag) == ncol(object) #> [1] TRUE head(low_depth_flag) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE   # Separate calculation of technical failure flag. tech_failure_flag <- h_tech_failure_flag(object, control_quality(min_corr = 0.35)) length(tech_failure_flag) == ncol(object) #> [1] TRUE head(tech_failure_flag) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_tech_failure(object)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_depth(object)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE           TRUE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_expression(object)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>            FALSE             TRUE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":null,"dir":"Reference","previous_headings":"","what":"Query Gene Annotations from a Connection — query","title":"Query Gene Annotations from a Connection — query","text":"generic function query() interface querying gene annotations data base connection.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query Gene Annotations from a Connection — query","text":"","code":"query(genes, connection)  # S4 method for character,ConnectionBiomart query(genes, connection)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query Gene Annotations from a Connection — query","text":"genes (character) gene IDs. connection (connection class) data base connection object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query Gene Annotations from a Connection — query","text":"S4Vectors::DataFrame gene annotations. required : rownames identical input genes. colnames equal annotation columns .row_data_annotation_cols. Therefore, missing information needs properly included DataFrame NA entries.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Query Gene Annotations from a Connection — query","text":"method provided ConnectionBiomart class. However, framework extensible: simple add new connections corresponding query methods data bases, e.g. company internal data bases. Please make sure follow required format returned value. BioMart queries might return information genes. can due different versions used gene IDs queried Ensembl data base.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/query.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query Gene Annotations from a Connection — query","text":"","code":"if (interactive()) {   object <- hermes_data   connection <- connect_biomart(prefix(object))   result <- query(genes(object), connection)   head(result)   head(annotation(object)) }"},{"path":"https://insightsengineering.github.io/hermes/main/reference/rbind.html","id":null,"dir":"Reference","previous_headings":"","what":"Row Binding of AnyHermesData Objects — rbind","title":"Row Binding of AnyHermesData Objects — rbind","text":"method combines AnyHermesData objects samples different features interest (rows assays).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rbind.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row Binding of AnyHermesData Objects — rbind","text":"... (AnyHermesData) objects row bind.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rbind.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Row Binding of AnyHermesData Objects — rbind","text":"combined AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rbind.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Row Binding of AnyHermesData Objects — rbind","text":"Note just inherits SummarizedExperiment::rbind,SummarizedExperiment-method(). binding AnyHermesData object SummarizedExperiment::SummarizedExperiment object, result SummarizedExperiment::SummarizedExperiment object (general class). Note need unique gene IDs (row names) prefix across combined object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/rbind.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Row Binding of AnyHermesData Objects — rbind","text":"","code":"a <- hermes_data[1:2542, ] b <- hermes_data[2543:5085, ] result <- rbind(a, b) class(result) #> [1] \"HermesData\" #> attr(,\"package\") #> [1] \"hermes\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rename.html","id":null,"dir":"Reference","previous_headings":"","what":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"method renames columns rowData colData, well assays, SummarizedExperiment::SummarizedExperiment objects. increases flexibility since renaming can done conversion HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"","code":"# S4 method for SummarizedExperiment rename(   x,   row_data = character(),   col_data = character(),   assays = character(),   ... )  # S4 method for data.frame rename(x, ...)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/rename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"x (SummarizedExperiment) object rename contents . row_data (named character) mapping existing (right-hand side values) new (left-hand side names) column names rowData. col_data (named character) mapping existing (right-hand side values) new (left-hand side names) column names colData. assays (named character) mapping existing (right-hand side values) new (left-hand side names) assay names. ... additional arguments (used ).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"SummarizedExperiment::SummarizedExperiment object renamed contents.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/rename.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"","code":"x <- summarized_experiment # Use deliberately a non-standard assay name in this example. assayNames(x) <- \"count\"  # Rename `HGNC` to `symbol` in the `rowData`. x <- rename(x, row_data = c(symbol = \"HGNC\")) head(names(rowData(x))) #> [1] \"symbol\"       \"HGNCGeneName\" \"GeneID\"       \"Chromosome\"   \"StartBP\"      #> [6] \"EndBP\"         # Rename `LowDepthFlag` to `low_depth_flag` in `colData`. x <- rename(x, col_data = c(low_depth_flag = \"LowDepthFlag\")) tail(names(colData(x))) #> [1] \"ALIVDT\"               \"COHORT\"               \"TTYPE\"                #> [4] \"STDSSDY\"              \"low_depth_flag\"       \"TechnicalFailureFlag\"  # Rename assay `count` to `counts`. x <- rename(x, assays = c(counts = \"count\")) assayNames(x) #> [1] \"counts\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/samples.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample IDs Accessor — samples,AnyHermesData-method","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"Access sample IDs, .e. col names, AnyHermesData object nicely named accessor method.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/samples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"","code":"# S4 method for AnyHermesData samples(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/samples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/samples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"character vector sample IDs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/samples.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"","code":"a <- hermes_data samples(a) #>  [1] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" #>  [5] \"06520092C0017R\" \"06520103C0017R\" \"06520001B0023R\" \"06520022C0017R\" #>  [9] \"06520062C0017R\" \"06520046C0018R\" \"06520101B0017R\" \"06520047C0017R\" #> [13] \"06520024B0014R\" \"06520080B0023R\" \"06520093C0017R\" \"06520070C0018R\" #> [17] \"06520023C0018R\" \"06520099B0017R\" \"06520015C0016R\" \"06520019C0023R\""},{"path":"https://insightsengineering.github.io/hermes/main/reference/set_tech_failure.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Technical Failure Flags — set_tech_failure","title":"Set Technical Failure Flags — set_tech_failure","text":"Setter function allows user define sample manually technical failure.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/set_tech_failure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Technical Failure Flags — set_tech_failure","text":"","code":"set_tech_failure(object, sample_ids)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/set_tech_failure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Technical Failure Flags — set_tech_failure","text":"object (AnyHermesData) input. sample_ids (character)  sample IDs flagged technical failures.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/set_tech_failure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Technical Failure Flags — set_tech_failure","text":"AnyHermesData object modified technical failure flags.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/set_tech_failure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Technical Failure Flags — set_tech_failure","text":"","code":"# Manually flag technical failures in a `AnyHermesData` object. object <- hermes_data get_tech_failure(object)[\"06520101B0017R\"] #> 06520101B0017R  #>          FALSE  result <- set_tech_failure(object, c(\"06520101B0017R\", \"06520047C0017R\")) get_tech_failure(result)[\"06520101B0017R\"] #> 06520101B0017R  #>           TRUE"},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":null,"dir":"Reference","previous_headings":"","what":"Show Method for AnyHermesData Objects — show,HermesData-method","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"show method displays high-level information AnyHermesData objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"","code":"# S4 method for HermesData show(object)  # S4 method for RangedHermesData show(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"None (invisible NULL), used side effect printing console.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"method used HermesData RangedHermesData objects. need define separately method used instead one inherited SummarizedExperiment::SummarizedExperiment.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/show.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"","code":"object <- hermes_data object #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY"},{"path":"https://insightsengineering.github.io/hermes/main/reference/subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Subsetting AnyHermesData Objects — subset","title":"Subsetting AnyHermesData Objects — subset","text":"method subsets AnyHermesData objects, based expressions involving rowData columns colData columns.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subsetting AnyHermesData Objects — subset","text":"x (AnyHermesData) object subset . subset (expression) logical expression based rowData columns select genes. select (expression) logical expression based colData columns select samples.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subsetting AnyHermesData Objects — subset","text":"subsetted AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/subset.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subsetting AnyHermesData Objects — subset","text":"Note just inherits SummarizedExperiment::subset,SummarizedExperiment-method().","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/subset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subsetting AnyHermesData Objects — subset","text":"","code":"a <- hermes_data a #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset both genes and samples. subset(a, subset = low_expression_flag, select = DISCSTUD == \"N\") #> class: HermesData #> assays(1): counts #> genes(3021): GeneID:10677 GeneID:101928428 ... GeneID:9084 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(6): 06520067C0018R 06520105C0017R ... 06520023C0018R #>   06520099B0017R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset only genes. subset(a, subset = chromosome == \"2\") #> class: HermesData #> assays(1): counts #> genes(326): GeneID:101929282 GeneID:51455 ... GeneID:101927614 #>   GeneID:285172 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset only samples. subset(a, select = AGE > 18) #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(4): 06520011B0023R 06520103C0017R 06520001B0023R 06520080B0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY"},{"path":"https://insightsengineering.github.io/hermes/main/reference/summarized_experiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Example SummarizedExperiment Data — summarized_experiment","title":"Example SummarizedExperiment Data — summarized_experiment","text":"example SummarizedExperiment::SummarizedExperiment can used create HermesData object. already contains required columns rowData colData.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summarized_experiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example SummarizedExperiment Data — summarized_experiment","text":"","code":"summarized_experiment"},{"path":"https://insightsengineering.github.io/hermes/main/reference/summarized_experiment.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example SummarizedExperiment Data — summarized_experiment","text":"SummarizedExperiment::SummarizedExperiment object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summarized_experiment.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example SummarizedExperiment Data — summarized_experiment","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary Method for AnyHermesData Objects — summary","title":"Summary Method for AnyHermesData Objects — summary","text":"Provides concise summary content AnyHermesData objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary Method for AnyHermesData Objects — summary","text":"","code":"summary(object, ...)  # S4 method for AnyHermesData summary(object)  # S4 method for HermesDataSummary show(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary Method for AnyHermesData Objects — summary","text":"object (HermesDataSummary)  result summary method applied AnyHermesData object. ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary Method for AnyHermesData Objects — summary","text":"object corresponding summary class, HermesDataSummary.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Summary Method for AnyHermesData Objects — summary","text":"summary(AnyHermesData): summary method AnyHermesData object creates HermesDataSummary object. show(HermesDataSummary): show method prints summary description HermesDataSummary object generated summary() method.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary Method for AnyHermesData Objects — summary","text":"","code":"object <- hermes_data object_summary <- summary(object)  # We can access parts of this S4 object with the `slot` function. str(object_summary) #> Formal class 'HermesDataSummary' [package \"hermes\"] with 10 slots #>   ..@ class_name            : chr \"HermesData\" #>   ..@ n_genes               : int 5085 #>   ..@ n_samples             : int 20 #>   ..@ additional_gene_info  : chr [1:3] \"GeneID\" \"SYMBOL\" \"chromosome_name\" #>   ..@ additional_sample_info: chr [1:72] \"Filename\" \"SampleID\" \"AGEGRP\" \"AGE18\" ... #>   ..@ no_qc_flags_filled    : logi FALSE #>   ..@ genes_fail            : chr [1:3021] \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" \"GeneID:102466731\" ... #>   ..@ samples_fail          : chr [1:2] \"06520063C0043R\" \"06520062C0017R\" #>   ..@ lib_sizes             : Named num [1:20] 5474927 5154958 4632496 5533212 5026848 ... #>   .. ..- attr(*, \"names\")= chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ... #>   ..@ assay_names           : chr \"counts\" slotNames(object_summary) #>  [1] \"class_name\"             \"n_genes\"                \"n_samples\"              #>  [4] \"additional_gene_info\"   \"additional_sample_info\" \"no_qc_flags_filled\"     #>  [7] \"genes_fail\"             \"samples_fail\"           \"lib_sizes\"              #> [10] \"assay_names\"            slot(object_summary, \"lib_sizes\") #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>        5474927        5154958        4632496        5533212        5026848  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520046C0018R  #>        7262374        6408552        5286953        4778014        4990556  #> 06520101B0017R 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R  #>        4923925        5417510        5560720        4642530        5016838  #> 06520070C0018R 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>        6464043        6080233        5314431        5426566        6139497   # Just calling the summary method like this will use the `show()` method. summary(object) #> HermesData object with 20 samples of 5085 genes. #> - Library sizes across samples: mean 5476759, median 5365970, range 4632496 to 7262374 #> - Included assays (1): counts #> - Additional gene information (3): GeneID SYMBOL chromosome_name #> - Additional sample information (72): Filename SampleID ... TTYPE #>   STDSSDY #> - Low expression genes (3021): GeneID:10677 GeneID:101928428 ... #>   GeneID:9084 GeneID:9426 #> - Samples with too low depth or technical failures (2): 06520063C0043R #>   06520062C0017R"},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivation of Top Genes — top_genes","title":"Derivation of Top Genes — top_genes","text":"top_genes() creates HermesDataTopGenes object, extends data.frame. contains two columns: expression: containing statistic values calculated summary_fun across columns. name: gene names. corresponding autoplot() method visualizes result barplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivation of Top Genes — top_genes","text":"","code":"top_genes(   object,   assay_name = \"counts\",   summary_fun = rowMeans,   n_top = if (is.null(min_threshold)) 10L else NULL,   min_threshold = NULL )  # S4 method for HermesDataTopGenes autoplot(   object,   x_lab = \"HGNC gene names\",   y_lab = paste0(object@summary_fun_name, \"(\", object@assay_name, \")\"),   title = \"Top most expressed genes\" )"},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivation of Top Genes — top_genes","text":"object (AnyHermedData) input. assay_name (string) name assay use sorting genes. summary_fun (function) summary statistics function apply across samples assay resulting numeric vector one value per gene. n_top (count NULL) selection criteria based number entries. min_threshold (number NULL ) selection criteria based minimum summary statistics threshold. x_lab (string) x-axis label. y_lab (string) y-axis label. title (string) plot title.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivation of Top Genes — top_genes","text":"HermesDataTopGenes object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derivation of Top Genes — top_genes","text":"data frame sorted descending order expression top entries according selection criteria included. Note exactly one arguments n_top min_threshold must provided.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Derivation of Top Genes — top_genes","text":"autoplot(HermesDataTopGenes): Creates bar plot HermesDataTopGenes object, y axis shows expression statistics top genes x-axis.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/top_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Derivation of Top Genes — top_genes","text":"","code":"object <- hermes_data  # Default uses average of raw counts across samples to rank genes. top_genes(object) #>              expression         name #> GeneID:2335   390085.60  GeneID:2335 #> GeneID:79026  302684.20 GeneID:79026 #> GeneID:4627    60247.10  GeneID:4627 #> GeneID:667     59502.90   GeneID:667 #> GeneID:26986   58479.75 GeneID:26986 #> GeneID:6218    57782.15  GeneID:6218 #> GeneID:6205    50484.85  GeneID:6205 #> GeneID:811     42460.70   GeneID:811 #> GeneID:23215   41407.95 GeneID:23215 #> GeneID:4035    35884.20  GeneID:4035  # Instead of showing top 10 genes, can also set a minimum threshold on average counts. top_genes(object, n_top = NULL, min_threshold = 50000) #>              expression         name #> GeneID:2335   390085.60  GeneID:2335 #> GeneID:79026  302684.20 GeneID:79026 #> GeneID:4627    60247.10  GeneID:4627 #> GeneID:667     59502.90   GeneID:667 #> GeneID:26986   58479.75 GeneID:26986 #> GeneID:6218    57782.15  GeneID:6218 #> GeneID:6205    50484.85  GeneID:6205  # We can also use the maximum of raw counts across samples, by specifying a different # summary statistics function. result <- top_genes(object, summary_fun = rowMax)  # Finally we can produce barplots based on the results. autoplot(result, title = \"My top genes\")  autoplot(result, y_lab = \"Counts\", title = \"My top genes\")"},{"path":"https://insightsengineering.github.io/hermes/main/reference/validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"functions used internally therefore exported. work SummarizedExperiment::SummarizedExperiment objects, AnyHermesData objects defined successfully passing validation checks.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"","code":"validate_counts(object)  validate_cols(required, actual)  validate_row_data(object)  validate_col_data(object)  validate_names(object)  validate_prefix(object)"},{"path":"https://insightsengineering.github.io/hermes/main/reference/validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"object (SummarizedExperiment) object validate. required (character) required column names. actual (actual) actual column names.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"character vector validation failure messages, NULL case validation passes.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/validate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"validate_counts(): validates first assay counts containing non-missing, integer, non-negative values. validate_cols(): validates required column names contained actual column names. validate_row_data(): validates object contains rowData required columns. validate_col_data(): validates object contains colData required columns. validate_names(): validates object contains row column names. validate_prefix(): validates object prefix string contains alphabetic characters.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/wrap_in_mae.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap in MAE — wrap_in_mae","title":"Wrap in MAE — wrap_in_mae","text":"helper function wraps SummarizedExperiment objects MultiAssayExperiment (MAE) object.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/wrap_in_mae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap in MAE — wrap_in_mae","text":"","code":"wrap_in_mae(x, name = deparse(substitute(x)))"},{"path":"https://insightsengineering.github.io/hermes/main/reference/wrap_in_mae.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap in MAE — wrap_in_mae","text":"x (SummarizedExperiment) input create MAE object . name (string) experiment name use MAE x.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/wrap_in_mae.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap in MAE — wrap_in_mae","text":"MAE object experiment x given name.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/reference/wrap_in_mae.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap in MAE — wrap_in_mae","text":"","code":"mae <- wrap_in_mae(summarized_experiment) mae[[\"summarized_experiment\"]] #> class: SummarizedExperiment  #> dim: 5085 20  #> metadata(0): #> assays(1): counts #> rownames(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> rowData names(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> colnames(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> colData names(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"miscellaneous-1-7-2-9000","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.7.2.9000","text":"Changed maintainer email address.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"enhancements-1-7-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.7.1","text":"New plotting function draw_heatmap produce heatmaps (normalized) counts.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"miscellaneous-1-7-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.7.1","text":"utility function df_cols_to_factor now also converts existing factors explicit missing levels. Version bump forcats dependency. Removed ggplot2 deprecation warning ..count...","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"enhancements-1-0-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.0.1","text":"Additional version argument connect_biomart specify Ensembl version.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"meta-1-0-0","dir":"Changelog","previous_headings":"","what":"Meta","title":"hermes 1.0.0","text":"First public release hermes package. Submission BioConductor.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"enhancements-1-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.0.0","text":"Better legends genes barplot correlation heatmap. Improved vignette layout using BioConductor style.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"miscellaneous-1-0-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.0.0","text":"New utility function cut_quantile cutting numeric vector quantiles. New utility function cat_with_newline concatenating printing newline. New check function check_proportion checks single proportion.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"new-features-0-1-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"hermes 0.1.1","text":"New function draw_scatterplot produce scatterplots two genes gene signatures. New function draw_boxplot boxplots gene expression values. New function draw_barplot barplots dichotomized gene expression counts two three percentile categories. New helper function wrap_in_mae wraps single SummarizedExperiment object MAE object. New method rename makes renaming columns rowData colData well assay names existing SummarizedExperiment objects much easier, step converting HermesData. New method lapply allows user apply function experiments MultiAssayExperiment. New method isEmpty checks whether SummarizedExperiment object empty. New gene filtering option n_top calc_pca function, allows filtering genes greatest variability across samples. New class GeneSpec specification genes gene signatures, see ?gene_spec simple construction. Inclusion gene signature functions colPrinComp1 colMeanZscores supplement standard column statistics functions. New helper function col_data_with_genes extracts sample variables saved colData together selected gene information combined data set. New helper function inner_join_cdisc joins genetic CDISC data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"hermes 0.1.1","text":"normalize() now also works hermes package loaded, .e. can use hermes::normalize(). correlate() now also works factor variables sample variables HermesData object. add_quality_flags() longer return NA technical failure flags samples single gene contained input, instead vector FALSE ensure correct downstream functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 0.1.1","text":"Updated LICENCE README new package references. multi_assay_experiment now contains HermesData experiments, different patient IDs, one experiment normalized assays, multiple samples per patient one experiment. main HermesData example now saved package hermes_data, previous summarized_experiment still available. Note patient IDs changed new version align multi_assay_experiment. Renaming required rowData colData columns consistent standards use lowercase snake-case names. Annotation querying setting now flexible also allows query annotations required ones. Instead gene starts ends, total length gene exons now used annotation column size. Corresponding queries BioMart used return gene size. df_char_to_factor deprecated (can still used warning) replaced df_cols_to_factor, also converts logical variables factor variables. providing SummarizedExperiment objects containing DelayedMatrix assays HermesData() constructor, silently converted matrix assays ensure downstream functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"hermes-010","dir":"Changelog","previous_headings":"","what":"hermes 0.1.0","title":"hermes 0.1.0","text":"First internal release hermes package, contains classes, methods functions import, quality-check, filter, normalize, analyze RNAseq counts data differential expression. hermes successor rnaseqTools R package. core functionality built BioConductor ecosystem, especially SummarizedExperiment class. New users first begin reading “Introduction hermes” vignette become familiar hermes concepts.","code":""},{"path":"https://insightsengineering.github.io/hermes/main/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"hermes 0.1.0","text":"Import RNAseq count data hermes ready format. Annotate gene information Ensembl database via biomaRt. Add quality control (QC) flags genes samples. Filter subset data set. Normalize counts. Produce descriptive plots. Perform principal components analysis. Produce templated QC Rmd report. Perform differential expression analysis.","code":""}]
+[{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/hermes/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"acknowledgments","dir":"Articles","previous_headings":"","what":"Acknowledgments","title":"Introduction to `hermes`","text":"hermes successor Roche internal rnaseqTools R package, therefore many code ideas borrowed . Therefore like thank rnaseqTools authors work. particular, like acknowledge Chendi Liao Joe Paulson guidance explanations development hermes. also discussed class design Valerie Obenchain, discussed RNAseq data standards Armen Karapetyan. borrowed ideas Roche internal biokitr R package discussed maintainer Daniel Marbach. Finally, hermes originated part NEST project. grateful entire team’s support. Thanks lot everyone involved!","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to `hermes`","text":"First let’s see can install hermes package.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"bioconductor","dir":"Articles","previous_headings":"Installation","what":"BioConductor","title":"Introduction to `hermes`","text":"development version (3.15) BioConductor, can install current package version :","code":"if (!require(\"BiocManager\")) {   install.packages(\"BiocManager\") } BiocManager::install(\"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"github","dir":"Articles","previous_headings":"Installation","what":"GitHub","title":"Introduction to `hermes`","text":"can install unstable development version GitHub :","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } devtools::install_github(\"insightsengineering/hermes\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction to `hermes`","text":"hermes R package provides classes, methods functions import, quality-check, filter, normalize, analyze RNAseq counts data. core functionality built BioConductor ecosystem, especially SummarizedExperiment. vignette read new users package. vignette going learn : Import RNAseq count data hermes ready format. Annotate gene information automatically central database (e.g. BioMart). Add quality control (QC) flags genes samples. Filter data set. Normalize counts. Quickly produce descriptive plots. Perform principal components analysis. Produce templated QC report. Perform differential expression analysis. packages used vignette : datasets used vignette :","code":"library(hermes) library(SummarizedExperiment) ?expression_set ?summarized_experiment"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"importing-data","dir":"Articles","previous_headings":"","what":"Importing Data","title":"Introduction to `hermes`","text":"data hermes needs imported HermesData RangedHermesData format.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"importing-a-summarizedexperiment","dir":"Articles","previous_headings":"Importing Data","what":"Importing a SummarizedExperiment","title":"Introduction to `hermes`","text":"simplest way import data SummarizedExperiment (SE) object. HermesData object just special SE, additional requirements slots. nutshell, object needs counts assay, certain gene sample variables, unique row column names. row names, .e. gene names, must start common prefix GeneID ENSG enable easy annotations. See ?HermesData detailed requirements. SE follows minimum conventions, can just call HermesData constructor : HermesData object. Note case deprecated names used rowData colData variables, therefore appear “additional” gene sample information. However can still call default constructor new names filled missing values, e.g.: want map old column names new column names avoid duplication new missing value columns, can using rename() method. example : example can now see annotations successfully carried information since mapped old annotations new required names : bit details can also call summary() object. , let’s use already prepared HermesData object. Likewise, receive error “‘counts’ assay found”, can use rename() function change name assay SummarizedExperiment object counts. example, following object type SummarizedExperiment assay name count, produce assay name error: use following code convert assay name counts, making able convert HermesData object:","code":"object <- HermesData(summarized_experiment) object #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                     symbol      desc chromosome      size #>                  <logical> <logical>  <logical> <logical> #> GeneID:11185            NA        NA         NA        NA #> GeneID:10677            NA        NA         NA        NA #> GeneID:101928428        NA        NA         NA        NA #> GeneID:100422835        NA        NA         NA        NA #> GeneID:102466731        NA        NA         NA        NA #> GeneID:64881            NA        NA         NA        NA object <- summarized_experiment %>%   rename(     row_data = c(       symbol = \"HGNC\",       desc = \"HGNCGeneName\",       chromosome = \"Chromosome\",       size = \"WidthBP\",       low_expression_flag = \"LowExpressionFlag\"     ),     col_data = c(       low_depth_flag = \"LowDepthFlag\",       technical_failure_flag = \"TechnicalFailureFlag\"     )   ) %>%   HermesData() head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                        symbol                   desc  chromosome      size #>                   <character>            <character> <character> <integer> #> GeneID:11185             INMT indolethylamine N-me..           7      5468 #> GeneID:10677             AVIL               advillin          12     18694 #> GeneID:101928428 LOC101928428 RNA-binding protein ..  GL000220.1       138 #> GeneID:100422835      MIR3183          microRNA 3183          17        84 #> GeneID:102466731     MIR6769A         microRNA 6769a          16        73 #> GeneID:64881           PCDH20       protocadherin 20          13      5838 summary(object) #> HermesData object with 20 samples of 5085 genes. #> - Library sizes across samples: mean 5476759, median 5365970, range 4632496 to 7262374 #> - Included assays (1): counts #> - Additional gene information (7): GeneID StartBP ... SYMBOL #>   chromosome_name #> - Additional sample information (73): Filename SampleID ... STDSSDY #>   technical_failure_flag #> - Low expression genes (3021): GeneID:10677 GeneID:101928428 ... #>   GeneID:9084 GeneID:9426 #> - Samples with too low depth or technical failures (20): NA NA ... NA #>   NA object <- hermes_data object_exp <- summarized_experiment %>%   rename(assays = c(count = \"counts\")) object_exp <- rename(object_exp,   assays = c(counts = \"count\") ) object_exp <- HermesData(object_exp)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"importing-an-expressionset","dir":"Articles","previous_headings":"Importing Data","what":"Importing an ExpressionSet","title":"Introduction to `hermes`","text":"start ExpressionSet, can first convert RangedSummarizedExperiment import RangedHermesData:","code":"se <- makeSummarizedExperimentFromExpressionSet(expression_set) object2 <- HermesData(se) object2 #> class: RangedHermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"importing-a-matrix","dir":"Articles","previous_headings":"Importing Data","what":"Importing a Matrix","title":"Introduction to `hermes`","text":"general can also import matrix counts. just pass required gene sample information data frames constructor. Note can easily access counts assay (matrix) final object counts():","code":"counts_matrix <- assay(hermes_data) object3 <- HermesDataFromMatrix(   counts = counts_matrix,   rowData = rowData(hermes_data),   colData = colData(hermes_data) ) object3 #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY identical(object, object3) #> [1] TRUE cnts <- counts(object) cnts[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185                  3             66             35 #> GeneID:10677               1668            236             95 #> GeneID:101928428              0              0              0"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"annotations","dir":"Articles","previous_headings":"","what":"Annotations","title":"Introduction to `hermes`","text":"hermes provides modular approach querying gene annotations, order allow future extensions downstream packages.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"connection-to-database","dir":"Articles","previous_headings":"Annotations","what":"Connection to Database","title":"Introduction to `hermes`","text":"first step connect database. hermes option currently databases utilize BioMart software suite. However due generic function design, simple extend hermes data base connections. order save time vignette build, zoom subset original object containing first 10 genes. corresponding function takes common gene ID prefix argument determine format gene IDs filter variable use query later . using prefix() method access prefix saved HermesData object.","code":"small_object <- object[1:10, ] httr::set_config(httr::config(ssl_verifypeer = 0L)) connection <- connect_biomart(prefix(small_object))"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"querying-and-saving-annotations","dir":"Articles","previous_headings":"Annotations","what":"Querying and Saving Annotations","title":"Introduction to `hermes`","text":"second step query gene annotations save object. using genes() method access gene IDs (row names) HermesData object. Note genes might found data base corresponding rows NA annotations.","code":"annotation(small_object) <- query(genes(small_object), connection)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"quality-control-flags","dir":"Articles","previous_headings":"","what":"Quality Control Flags","title":"Introduction to `hermes`","text":"hermes provides automatic gene sample flagging, well manual sample flagging functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"automatic-gene-and-sample-flagging","dir":"Articles","previous_headings":"Quality Control Flags","what":"Automatic Gene and Sample Flagging","title":"Introduction to `hermes`","text":"genes, counted many samples don’t pass minimum expression CPM (counts per million reads mapped) threshold. many, gene flagged “low expression” gene. samples, two flags provided. “technical failure” flag based average Pearson correlation samples. “low depth” flag based library size, .e. total sum counts sample across genes. Thresholds flags can initialized control_quality(), flags added add_quality_flags().","code":"my_controls <- control_quality(min_cpm = 10, min_cpm_prop = 0.4, min_corr = 0.4, min_depth = 1e4) #> Loading required namespace: testthat object_flagged <- add_quality_flags(object, control = my_controls)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"manual-sample-flagging","dir":"Articles","previous_headings":"Quality Control Flags","what":"Manual Sample Flagging","title":"Introduction to `hermes`","text":"Sometimes necessary manually flag certain samples technical failures, e.g. looking one analyses discussed . possible, .","code":"object_flagged <- set_tech_failure(object_flagged, sample_ids = \"06520011B0023R\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"accessing-flags","dir":"Articles","previous_headings":"Quality Control Flags","what":"Accessing Flags","title":"Introduction to `hermes`","text":"flags access functions.","code":"head(get_tech_failure(object_flagged)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>           TRUE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE head(get_low_depth(object_flagged)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE head(get_low_expression(object_flagged)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>             TRUE            FALSE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"filtering-data","dir":"Articles","previous_headings":"","what":"Filtering Data","title":"Introduction to `hermes`","text":"can either filter based default QC flags, based custom variables gene sample information.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"based-on-default-qc-flags","dir":"Articles","previous_headings":"Filtering Data","what":"Based on Default QC Flags","title":"Introduction to `hermes`","text":"simple filter() function. also possible selectively filter genes samples using argument.","code":"object_flagged_filtered <- filter(object_flagged) object_flagged_genes_filtered <- filter(object_flagged, what = \"genes\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"based-on-custom-variables","dir":"Articles","previous_headings":"Filtering Data","what":"Based on Custom Variables","title":"Introduction to `hermes`","text":"can done subset() function. Genes can filtered subset argument via expressions using gene information variables, samples can filtered select argument using sample information variables. order see ones available can queries first.","code":"names(rowData(object_flagged)) #> [1] \"symbol\"              \"desc\"                \"GeneID\"              #> [4] \"chromosome\"          \"size\"                \"SYMBOL\"              #> [7] \"chromosome_name\"     \"low_expression_flag\" names(colData(object_flagged)) #>  [1] \"Filename\"          \"SampleID\"          \"AGEGRP\"            #>  [4] \"AGE18\"             \"STDDRS\"            \"STDDRSD\"           #>  [7] \"STDSSDT\"           \"TRTDRS\"            \"TRTDRSD\"           #> [10] \"BHDCIRC\"           \"BHDCIRCU\"          \"ADAFL\"             #> [13] \"BLANP\"             \"BKPS\"              \"BLKS\"              #> [16] \"BTANNER\"           \"FRPST\"             \"DURIDX\"            #> [19] \"DURSAF\"            \"DURSUR\"            \"LNTHRPY\"           #> [22] \"AENCIFL\"           \"STUDYID\"           \"USUBJID\"           #> [25] \"RFSTDTC\"           \"RFENDTC\"           \"RFXSTDTC\"          #> [28] \"RFXENDTC\"          \"RFICDTC\"           \"RFPENDTC\"          #> [31] \"DTHDTC\"            \"DTHFL\"             \"SITEID\"            #> [34] \"INVID\"             \"AGE\"               \"AGEU\"              #> [37] \"SEX\"               \"RACE\"              \"ETHNIC\"            #> [40] \"ARMCD\"             \"ARM\"               \"ACTARMCD\"          #> [43] \"ACTARM\"            \"COUNTRY\"           \"DMDTC\"             #> [46] \"DMDY\"              \"BAGE\"              \"BAGEU\"             #> [49] \"BWT\"               \"BWTU\"              \"BHT\"               #> [52] \"BHTU\"              \"BBMI\"              \"ITTFL\"             #> [55] \"SAFFL\"             \"INFCODT\"           \"RANDDT\"            #> [58] \"TRTSDTC\"           \"TRTSDTM\"           \"TRTSTMF\"           #> [61] \"TRTEDTM\"           \"TRTETMF\"           \"TRTDUR\"            #> [64] \"DISCSTUD\"          \"DISCDEAT\"          \"DISCAE\"            #> [67] \"DISTRTFL\"          \"AEWITHFL\"          \"ALIVDT\"            #> [70] \"COHORT\"            \"TTYPE\"             \"STDSSDY\"           #> [73] \"low_depth_flag\"    \"tech_failure_flag\" head(rowData(object_flagged)$chromosome) #> [1] \"7\"          \"12\"         \"GL000220.1\" \"17\"         \"16\"         #> [6] \"13\" head(object_flagged$ARMCD) #> [1] \"COH1\"  \"COH1\"  \"COH8\"  \"COH12\" \"COH9O\" \"COH9E\" object_flagged_subsetted <- subset(   object_flagged,   subset = chromosome == \"5\",   select = ARMCD == \"COH1\" )"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"normalizing-counts","dir":"Articles","previous_headings":"","what":"Normalizing Counts","title":"Introduction to `hermes`","text":"Normalizing counts within samples (CPM), genes (RPKM) across (TPM) can achieved normalize() function. normalize() function can also transform counts variance stabilizing transformation (vst) regularized log transformation (rlog) proposed DESeq2 package. corresponding assays saved object can accessed assay(). used control settings can accessed afterwards metadata object: Note also filtering settings saved . custom normalization options, use control_normalize(). example, use log scale original scale counts:","code":"object_normalized <- normalize(object_flagged_filtered) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. object_rlog_normalized <- normalize(object_flagged_filtered, \"rlog\") #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. assay(object_normalized, \"tpm\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677        4.096418       3.323016       7.714990 #> GeneID:286205       2.985506       3.182624       3.769962 #> GeneID:8365        11.711741      12.421108      12.466491 assay(object_rlog_normalized, \"rlog\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677        8.101651       7.153488      10.281393 #> GeneID:286205      10.101287       9.859074      10.104426 #> GeneID:8365        10.023097      10.163191       9.935722 metadata(object_normalized) #> $control_quality_flags #> $control_quality_flags$min_cpm #> [1] 10 #>  #> $control_quality_flags$min_cpm_prop #> [1] 0.4 #>  #> $control_quality_flags$min_corr #> [1] 0.4 #>  #> $control_quality_flags$min_depth #> [1] 10000 #>  #>  #> $control_normalize #> $control_normalize$log #> [1] TRUE #>  #> $control_normalize$lib_sizes #> NULL #>  #> $control_normalize$prior_count #> [1] 1 #>  #> $control_normalize$fit_type #> [1] \"parametric\" object_normalized_original <- normalize(   object_flagged_filtered,   control = control_normalize(log = FALSE) ) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. assay(object_normalized_original, \"tpm\")[1:3, 1:3] #>               06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:10677       16.105854       9.007544       209.1084 #> GeneID:286205       6.920033       8.079569        12.6418 #> GeneID:8365      3353.172671    5483.360511      5658.6256"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"simple-plots","dir":"Articles","previous_headings":"Descriptive Plots","what":"Simple Plots","title":"Introduction to `hermes`","text":"series simple descriptive plots can obtained just calling autoplot() object.  Note individual plots can produced series draw_*() functions, see ?plot_all detailed list. , can customized . example, can change number color bins library size histogram:","code":"autoplot(object) draw_libsize_hist(object, bins = 10L, fill = \"blue\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"top-genes","dir":"Articles","previous_headings":"Descriptive Plots","what":"Top Genes","title":"Introduction to `hermes`","text":"Top genes can calculated visualized barplot.  passing another summary function, also variability can ranked example.","code":"most_expr_genes <- top_genes(object_normalized, assay_name = \"tpm\") autoplot(most_expr_genes) most_var_genes <- top_genes(object_normalized, summary_fun = rowSds) autoplot(most_var_genes)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"heatmap-of-genes-among-samples","dir":"Articles","previous_headings":"Descriptive Plots","what":"Heatmap of Genes among Samples","title":"Introduction to `hermes`","text":"Relative expression genes can displayed using heatmap  heatmap can grouped labels HermesData object, \"COUNTRY\" \"AGEGRP\".","code":"draw_heatmap(object[1:20], assay_name = \"counts\") draw_heatmap(object[1:20], assay_name = \"counts\", col_data_annotation = \"COUNTRY\")"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"correlation-between-samples","dir":"Articles","previous_headings":"Descriptive Plots","what":"Correlation between Samples","title":"Introduction to `hermes`","text":"sample correlation matrix samples can obtained correlate() function. can visualized heatmap using autoplot() . See ?calc_cor detailed options.","code":"cor_mat <- correlate(object) autoplot(cor_mat)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"principal-components","dir":"Articles","previous_headings":"","what":"Principal Components","title":"Introduction to `hermes`","text":"Let’s see can perform Principal Components Analysis (PCA).","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"pca-of-samples","dir":"Articles","previous_headings":"Principal Components","what":"PCA of Samples","title":"Introduction to `hermes`","text":"PCA can performed calc_pca(). result can summarized plotted.  Note various options available plot, example can look different principal components, color samples sample variables. See ?ggfortify::autoplot.prcomp details.","code":"pca_res <- calc_pca(object_normalized, assay_name = \"tpm\") summary(pca_res)$importance #>                             PC1      PC2      PC3      PC4      PC5      PC6 #> Standard deviation     22.08095 17.34762 15.19930 12.80689 11.76153 10.48121 #> Proportion of Variance  0.24066  0.14854  0.11403  0.08096  0.06828  0.05422 #> Cumulative Proportion   0.24066  0.38919  0.50322  0.58418  0.65246  0.70668 #>                             PC7      PC8      PC9     PC10     PC11     PC12 #> Standard deviation     9.812505 8.950926 8.530826 8.196006 7.905973 7.216002 #> Proportion of Variance 0.047520 0.039550 0.035920 0.033160 0.030850 0.025700 #> Cumulative Proportion  0.754200 0.793750 0.829670 0.862830 0.893680 0.919380 #>                           PC13     PC14     PC15     PC16     PC17              #> Standard deviation     6.92755 6.532485 5.501383 5.151959 3.983283 2.280611e-14 #> Proportion of Variance 0.02369 0.021060 0.014940 0.013100 0.007830 0.000000e+00 #> Cumulative Proportion  0.94307 0.964130 0.979070 0.992170 1.000000 1.000000e+00 autoplot(pca_res) autoplot(   pca_res,   x = 2, y = 3,   data = as.data.frame(colData(object_normalized)), colour = \"SEX\" )"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"correlation-with-sample-variables","dir":"Articles","previous_headings":"Principal Components","what":"Correlation with Sample Variables","title":"Introduction to `hermes`","text":"Subsequently easy correlate obtained principal components sample variables. obtain matrix R-squared (R2) values combinations, can visualized heatmap. See ?pca_cor_samplevar details.","code":"pca_cor <- correlate(pca_res, object_normalized) autoplot(pca_cor)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"qc-report-template","dir":"Articles","previous_headings":"","what":"QC Report Template","title":"Introduction to `hermes`","text":"order quickly obtain quality control report new RNAseq data set, can proceed follows. Save input SummarizedExperiment using R’s save() function binary data file (e.g. ending .rda suffix). Load hermes package RStudio click : File > New File > R Markdown > Template select QC report template hermes. Fill parameters yaml header, including required file paths input file , resulting HermesData object saved. Knit document. report contains mentioned descriptive plots PCA analyses can useful starting point analysis.","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"differential-expression","dir":"Articles","previous_headings":"","what":"Differential Expression","title":"Introduction to `hermes`","text":"addition QC analyses, simple differential expression analysis supported hermes. addition filtered object (normalization counts required) variable name factor contrast samples needs provided diff_expression(). Note use utility function df_cols_to_factor() converts default character logical variables factor variables. one possible way ensure utilized group variable factor. Afterwards standard volcano plot can produced.","code":"colData(object) <- df_cols_to_factor(colData(object)) diff_res <- diff_expression(object, group = \"SEX\", method = \"voom\") head(diff_res) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -4.239244 0.0004209192 0.9118348 #> GeneID:51227  -1.0467295 -4.032550 0.0006788432 0.9118348 #> GeneID:344558  1.6896266  3.824046 0.0010993677 0.9118348 #> GeneID:51575  -0.7760844 -3.746293 0.0013155805 0.9118348 #> GeneID:151242 -3.4358998 -3.570103 0.0019741997 0.9118348 #> GeneID:8904   -0.6100354 -3.542864 0.0021017199 0.9118348 autoplot(diff_res, log2_fc_thresh = 8)"},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to `hermes`","text":"hermes R package provides classes, methods functions import, quality-check, filter, normalize analyze RNAseq counts data. particular, robust object-oriented framework allows easy extensions future address user feature requests. feedback welcome - thank much advance thoughts hermes!","code":""},{"path":"https://insightsengineering.github.io/hermes/articles/hermes.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Introduction to `hermes`","text":"output sessionInfo() system document compiled running pandoc 3.4:","code":"#> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] hermes_1.7.2.9003           SummarizedExperiment_1.36.0 #>  [3] Biobase_2.66.0              GenomicRanges_1.58.0        #>  [5] GenomeInfoDb_1.42.1         IRanges_2.40.1              #>  [7] S4Vectors_0.44.0            BiocGenerics_0.52.0         #>  [9] MatrixGenerics_1.18.0       matrixStats_1.4.1           #> [11] ggfortify_0.4.17            ggplot2_3.5.1               #> [13] BiocStyle_2.34.0            #>  #> loaded via a namespace (and not attached): #>   [1] Rdpack_2.6.2                DBI_1.2.3                   #>   [3] httr2_1.0.7                 gridExtra_2.3               #>   [5] testthat_3.2.2              biomaRt_2.62.0              #>   [7] rlang_1.1.4                 magrittr_2.0.3              #>   [9] clue_0.3-66                 GetoptLong_1.0.5            #>  [11] compiler_4.4.1              RSQLite_2.3.9               #>  [13] png_0.1-8                   systemfonts_1.1.0           #>  [15] vctrs_0.6.5                 stringr_1.5.1               #>  [17] pkgconfig_2.0.3             shape_1.4.6.1               #>  [19] crayon_1.5.3                fastmap_1.2.0               #>  [21] magick_2.8.5                dbplyr_2.5.0                #>  [23] backports_1.5.0             XVector_0.46.0              #>  [25] labeling_0.4.3              utf8_1.2.4                  #>  [27] rmarkdown_2.29              UCSC.utils_1.2.0            #>  [29] ragg_1.3.3                  purrr_1.0.2                 #>  [31] bit_4.5.0.1                 xfun_0.49                   #>  [33] MultiAssayExperiment_1.32.0 zlibbioc_1.52.0             #>  [35] cachem_1.1.0                jsonlite_1.8.9              #>  [37] progress_1.2.3              EnvStats_3.0.0              #>  [39] blob_1.2.4                  DelayedArray_0.32.0         #>  [41] BiocParallel_1.40.0         prettyunits_1.2.0           #>  [43] parallel_4.4.1              cluster_2.1.8               #>  [45] R6_2.5.1                    bslib_0.8.0                 #>  [47] stringi_1.8.4               RColorBrewer_1.1-3          #>  [49] limma_3.62.1                brio_1.1.5                  #>  [51] jquerylib_0.1.4             Rcpp_1.0.13-1               #>  [53] bookdown_0.41               assertthat_0.2.1            #>  [55] iterators_1.0.14            knitr_1.49                  #>  [57] Matrix_1.7-1                tidyselect_1.2.1            #>  [59] abind_1.4-8                 yaml_2.3.10                 #>  [61] doParallel_1.0.17           codetools_0.2-20            #>  [63] curl_6.0.1                  lattice_0.22-6              #>  [65] tibble_3.2.1                KEGGREST_1.46.0             #>  [67] withr_3.0.2                 evaluate_1.0.1              #>  [69] desc_1.4.3                  BiocFileCache_2.14.0        #>  [71] xml2_1.3.6                  Biostrings_2.74.0           #>  [73] circlize_0.4.16             filelock_1.0.3              #>  [75] pillar_1.9.0                BiocManager_1.30.25         #>  [77] checkmate_2.3.2             foreach_1.5.2               #>  [79] generics_0.1.3              hms_1.1.3                   #>  [81] munsell_0.5.1               scales_1.3.0                #>  [83] glue_1.8.0                  tools_4.4.1                 #>  [85] locfit_1.5-9.10             forcats_1.0.0               #>  [87] fs_1.6.5                    grid_4.4.1                  #>  [89] tidyr_1.3.1                 rbibutils_2.3               #>  [91] edgeR_4.4.1                 AnnotationDbi_1.68.0        #>  [93] colorspace_2.1-1            GenomeInfoDbData_1.2.13     #>  [95] cli_3.6.3                   rappdirs_0.3.3              #>  [97] textshaping_0.4.0           fansi_1.0.6                 #>  [99] S4Arrays_1.6.0              ComplexHeatmap_2.22.0       #> [101] dplyr_1.1.4                 gtable_0.3.6                #> [103] DESeq2_1.46.0               sass_0.4.9                  #> [105] digest_0.6.37               SparseArray_1.6.0           #> [107] ggrepel_0.9.6               farver_2.1.2                #> [109] rjson_0.2.23                htmlwidgets_1.6.4           #> [111] memoise_2.0.1               htmltools_0.5.8.1           #> [113] pkgdown_2.1.1               lifecycle_1.0.4             #> [115] httr_1.4.7                  statmod_1.5.0               #> [117] GlobalOptions_0.1.2         bit64_4.5.2"},{"path":"https://insightsengineering.github.io/hermes/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Namrata Bhatia. Author. Stefanie Bienert. Author. Benoit Falquet. Author. Haocheng Li. Author. Jeff Luong. Author. Lyndsee Midori Zhang. Author. Alex Richardson. Author. Simona Rossomanno. Author. Tim Treis. Author. Mark Yan. Author. Naomi Chang. Author. Chendi Liao. Author. Carolyn Zhang. Author. Joseph N. Paulson. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/hermes/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Bhatia N, Bienert S, Falquet B, Li H, Luong J, Midori Zhang L, Richardson , Rossomanno S, Treis T, Yan M, Chang N, Liao C, Carolyn Zhang, Paulson J (2024). hermes: Preprocessing, analyzing, reporting RNA-seq data. R package version 1.7.2.9003, https://insightsengineering.github.io/hermes/.","code":"@Manual{,   title = {hermes: Preprocessing, analyzing, and reporting of RNA-seq data},   author = {Daniel {Sabanés Bové} and Namrata Bhatia and Stefanie Bienert and Benoit Falquet and Haocheng Li and Jeff Luong and Lyndsee {Midori Zhang} and Alex Richardson and Simona Rossomanno and Tim Treis and Mark Yan and Naomi Chang and Chendi Liao and {Carolyn Zhang} and Joseph N. Paulson},   year = {2024},   note = {R package version 1.7.2.9003},   url = {https://insightsengineering.github.io/hermes/}, }"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/index.html","id":"bioconductor","dir":"","previous_headings":"Installation","what":"BioConductor","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can install current release BioConductor :","code":"if (!require(\"BiocManager\")) {   install.packages(\"BiocManager\") } BiocManager::install(\"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/index.html","id":"github","dir":"","previous_headings":"Installation","what":"GitHub","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can install development version GitHub :","code":"if (!require(\"devtools\")) {   install.packages(\"devtools\") } devtools::install_github(\"insightsengineering/hermes\")"},{"path":"https://insightsengineering.github.io/hermes/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"Preprocessing, analyzing, and reporting of RNA-seq data","text":"can get started reading introduction vignette:","code":"library(hermes) vignette(\"introduction\", package = \"hermes\")"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"GeneSpec consists gene IDs (possibly named labels), summary function name summary function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"GeneSpec$new() GeneSpec$get_genes() GeneSpec$get_gene_labels() GeneSpec$returns_vector() GeneSpec$get_label() GeneSpec$extract() GeneSpec$extract_data_frame() GeneSpec$clone()","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Creates new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$new(genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (named character NULL) gene IDs, names used labels available. fun (function NULL) summary function. NULL used multiple genes summarized returned matrix extract method. fun_name (string) name summary function.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-get-genes-","dir":"Reference","previous_headings":"","what":"Method get_genes()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_genes()"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-get-gene-labels-","dir":"Reference","previous_headings":"","what":"Method get_gene_labels()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns gene labels (substituted gene IDs available).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_gene_labels(genes = self$get_genes())"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (character) subset genes labels returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-returns-vector-","dir":"Reference","previous_headings":"","what":"Method returns_vector()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Predicate whether extract returns vector .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$returns_vector()"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-get-label-","dir":"Reference","previous_headings":"","what":"Method get_label()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Returns string can used e.g. plot labels.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$get_label(genes = self$get_genes())"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"genes (character) subset genes labels returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-extract-","dir":"Reference","previous_headings":"","what":"Method extract()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Extract gene values assay specified.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$extract(assay)"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"assay (matrix) original matrix rownames containing specified genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Either vector one value per column, matrix multiple genes rows.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-extract-data-frame-","dir":"Reference","previous_headings":"","what":"Method extract_data_frame()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"Extract gene values data.frame.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$extract_data_frame(assay)"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"assay (matrix) original matrix rownames containing specified genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"data.frame genes columns samples rows.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"GeneSpec$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/GeneSpec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class Representing a Gene (Signature) Specification — GeneSpec","text":"","code":"# Minimal specification if only one gene is used. x_spec <- gene_spec(\"GeneID:1820\")  # Using multiple genes with a signature. x_spec <- gene_spec(c(\"GeneID:1820\", \"GeneID:52\"), fun = colMeans) x_spec <- gene_spec(c(\"GeneID:1820\", \"GeneID:52\"), fun = colPrinComp1) x_spec$returns_vector() #> [1] TRUE x_spec$get_genes() #> [1] \"GeneID:1820\" \"GeneID:52\"   x_spec$get_gene_labels() #> [1] \"GeneID:1820\" \"GeneID:52\"   x_spec$get_label() #> [1] \"colPrinComp1(GeneID:1820, GeneID:52)\"  # Using multiple genes with partial labels, without a signature. x_spec <- gene_spec(c(A = \"GeneID:1820\", \"GeneID:52\")) x_spec$returns_vector() #> [1] FALSE x_spec$get_gene_labels() #> [1] \"A\"         \"GeneID:52\"  # Use the gene specification to extract genes from a matrix. mat <- matrix(   data = rpois(15, 10),   nrow = 3, ncol = 5,   dimnames = list(c(\"GeneID:1820\", \"GeneID:52\", \"GeneID:523\"), NULL) ) x_spec$extract(mat) #>           [,1] [,2] [,3] [,4] [,5] #> A            5   11    7   11   11 #> GeneID:52    6   13    9   16    7  # We can also extract these as a `data.frame`. x_spec$extract_data_frame(mat) #>    A GeneID.52 #> 1  5         6 #> 2 11        13 #> 3  7         9 #> 4 11        16 #> 5 11         7"},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"HermesData and RangedHermesData — HermesData-class","title":"HermesData and RangedHermesData — HermesData-class","text":"HermesData class extension SummarizedExperiment::SummarizedExperiment additional validation criteria.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HermesData and RangedHermesData — HermesData-class","text":"","code":"HermesData(object)  HermesDataFromMatrix(counts, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HermesData and RangedHermesData — HermesData-class","text":"object (SummarizedExperiment) input create HermesData object . RangedSummarizedExperiment, result RangedHermesData. counts (matrix) counts create HermesData object . ... additional arguments, e.g. rowData, colData, etc. passed SummarizedExperiment::SummarizedExperiment() internally. Note rowRanges passed instead rowData, result RangedHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"HermesData and RangedHermesData — HermesData-class","text":"object class AnyHermesData (HermesData RangedHermesData).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"HermesData and RangedHermesData — HermesData-class","text":"additional criteria : first assay must counts containing non-missing, integer, non-negative values. Note rename() can used edit assay name counts needed. following columns must rowData: symbol (also often called HGNC similar, example: \"INMT\") desc (gene name, example: \"indolethylamine N-methyltransferase\") chromosome (chromosome string, example: \"7\") size (size gene base pairs, e.g 5468) low_expression_flag (can populated add_quality_flags()) following columns must colData: low_depth_flag (can populated add_quality_flags()) tech_failure_flag (can populated add_quality_flags()) object must unique row column names. row names gene names column names sample names. Analogously, RangedHermesData extension SummarizedExperiment::RangedSummarizedExperiment additional validation requirements. Methods can defined classes time AnyHermesData signature. Biobase::ExpressionSet object can imported using SummarizedExperiment::makeSummarizedExperimentFromExpressionSet() function first convert SummarizedExperiment::SummarizedExperiment object converting HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"HermesData and RangedHermesData — HermesData-class","text":"prefix common prefix gene IDs (row names).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"HermesData and RangedHermesData — HermesData-class","text":"Note use S4Vectors::setValidity2() define validity method, allows us turn validity checks internal functions intermediate objects may valid within scope function. can helpful convert character logical variables factors colData() (HermesData creation). provide utility function df_cols_to_factor() simplify task, leave user allow full control details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/HermesData-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"HermesData and RangedHermesData — HermesData-class","text":"","code":"# Convert an `ExpressionSet` to a `RangedSummarizedExperiment`. ranged_summarized_experiment <- makeSummarizedExperimentFromExpressionSet(expression_set)  # Then convert to `RangedHermesData`. HermesData(ranged_summarized_experiment) #> class: RangedHermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag  # Create objects starting from a `SummarizedExperiment`. hermes_data <- HermesData(summarized_experiment) hermes_data #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag  # Create objects from a matrix. Note that additional arguments are not required but possible. counts_matrix <- assay(summarized_experiment) counts_hermes_data <- HermesDataFromMatrix(counts_matrix)"},{"path":"https://insightsengineering.github.io/hermes/reference/all_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks Whether All Missing — all_na","title":"Checks Whether All Missing — all_na","text":"Internal function check whether whole vector NA.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/all_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks Whether All Missing — all_na","text":"","code":"all_na(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/all_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks Whether All Missing — all_na","text":"x (vector) vector check.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/all_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks Whether All Missing — all_na","text":"Corresponding flag.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotation Accessor and Setter — annotation,AnyHermesData-method","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"methods access set gene annotations stored AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' annotation(object, ...)  .row_data_annotation_cols  # S4 method for class 'AnyHermesData,DataFrame' annotation(object) <- value"},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"annotation column names available exported character vector .row_data_annotation_cols.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"object (AnyHermesData) object access annotations . ... used. value (DataFrame) annotations replaced .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"S4Vectors::DataFrame gene annotations: symbol desc chromosome size","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"trying replace required annotations completely missing values genes, warning given corresponding gene IDs saved attribute annotation.missing.genes. Note also additional annotations beyond required ones may supplied stored.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotation Accessor and Setter — annotation,AnyHermesData-method","text":"","code":"object <- hermes_data head(annotation(object)) #> DataFrame with 6 rows and 4 columns #>                        symbol                   desc  chromosome      size #>                   <character>            <character> <character> <integer> #> GeneID:11185             INMT indolethylamine N-me..           7      5468 #> GeneID:10677             AVIL               advillin          12     18694 #> GeneID:101928428 LOC101928428 RNA-binding protein ..  GL000220.1       138 #> GeneID:100422835      MIR3183          microRNA 3183          17        84 #> GeneID:102466731     MIR6769A         microRNA 6769a          16        73 #> GeneID:64881           PCDH20       protocadherin 20          13      5838"},{"path":"https://insightsengineering.github.io/hermes/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for assert_that — assertions","title":"Additional Assertions for assert_that — assertions","text":"provide additional assertion functions can used together assertthat::assert_that().  provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional Assertions for assert_that — assertions","text":"","code":"is_class(x, class2)  is_hermes_data(x)  is_counts_vector(x)  is_list_with(x, elements)  one_provided(one, two)  is_constant(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional Assertions for assert_that — assertions","text":"x object check. class2 (character class definition) class x belong. elements (character) names elements list x. one first input. two second input.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for assert_that — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional Assertions for assert_that — assertions","text":"is_class(): checks class. is_hermes_data(): checks whether x AnyHermesData object. is_counts_vector(): checks vector counts (positive integers). is_list_with(): checks list containing elements. one_provided(): checks exactly one two inputs one, two NULL. is_constant(): checks whether vector x constant (supports numeric, factor, character, logical). NAs removed first.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/assertions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additional Assertions for assert_that — assertions","text":"","code":"# Assert a general class. a <- 5 is_class(a, \"character\") #> [1] FALSE  # Assert a `AnyHermesData` object. is_hermes_data(hermes_data) #> [1] TRUE is_hermes_data(42) #> [1] FALSE  # Assert a counts vector. a <- 5L is_counts_vector(a) #> [1] TRUE  # Assert a list containing certain elements. b <- list(a = 5, b = 3) is_list_with(b, c(\"a\", \"c\")) #> [1] FALSE is_list_with(b, c(\"a\", \"b\")) #> [1] TRUE  # Assert that exactly one of two arguments is provided. a <- 10 b <- 10 one_provided(a, b) #> [1] FALSE one_provided(a, NULL) #> [1] TRUE  # Assert a constant vector. is_constant(c(1, 2)) #> [1] FALSE is_constant(c(NA, 1)) #> [1] TRUE is_constant(c(\"a\", \"a\")) #> [1] TRUE is_constant(factor(c(\"a\", \"a\"))) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"correlate() method can calculate correlation matrix sample vectors counts specified assay. produces HermesDataCor object, extension matrix additional quality flags slot flag_data (containing tech_failure_flag low_depth_flag columns describing original input samples). autoplot() method afterwards can produce corresponding heatmap.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' correlate(object, assay_name = \"counts\", method = \"pearson\", ...)  # S4 method for class 'HermesDataCor' autoplot(   object,   flag_colors = c(`FALSE` = \"green\", `TRUE` = \"red\"),   cor_colors = circlize::colorRamp2(c(0, 0.5, 1), c(\"red\", \"yellow\", \"green\")),   ... )"},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"object (AnyHermesData) object calculate correlation. assay_name (string) name assay use. method (string) correlation method, see stats::cor() details. ... arguments passed ComplexHeatmap::Heatmap(). flag_colors (named character) vector specifies colors TRUE FALSE flag values. cor_colors (function) color scale function correlation values heatmap, produced circlize::colorRamp2().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"HermesDataCor object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"autoplot(HermesDataCor): autoplot() method uses ComplexHeatmap::Heatmap() function plot correlations samples saved HermesDataCor object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_cor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation between Sample Counts of AnyHermesData — correlate,AnyHermesData-method","text":"","code":"object <- hermes_data  # Calculate the sample correlation matrix. correlate(object) #> An object of class \"HermesDataCor\" #>                06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> 06520011B0023R      1.0000000      0.9609738      0.6473003      0.3904017 #> 06520067C0018R      0.9609738      1.0000000      0.6758462      0.4167789 #> 06520063C0043R      0.6473003      0.6758462      1.0000000      0.7742640 #> 06520105C0017R      0.3904017      0.4167789      0.7742640      1.0000000 #> 06520092C0017R      0.6633748      0.6604377      0.6113716      0.4520703 #> 06520103C0017R      0.9079581      0.8775734      0.5978126      0.4172803 #> 06520001B0023R      0.8818454      0.8570700      0.6658466      0.5111085 #> 06520022C0017R      0.9117386      0.9142934      0.8104461      0.6131335 #> 06520062C0017R      0.6753364      0.7157011      0.8896542      0.7652040 #> 06520046C0018R      0.3208473      0.3148823      0.4431801      0.3814626 #> 06520101B0017R      0.9314543      0.9041533      0.6417565      0.4319133 #> 06520047C0017R      0.6815391      0.6707660      0.5759576      0.4652142 #> 06520024B0014R      0.5835149      0.5819907      0.6588440      0.5231136 #> 06520080B0023R      0.5168947      0.5524994      0.8949026      0.8217901 #> 06520093C0017R      0.4138013      0.4497814      0.7953623      0.7202175 #> 06520070C0018R      0.4697837      0.5046432      0.8295754      0.8553639 #> 06520023C0018R      0.4033409      0.4404680      0.8266231      0.8575140 #> 06520099B0017R      0.4224672      0.4766716      0.7936238      0.6681055 #> 06520015C0016R      0.8093514      0.8036729      0.7640655      0.6482306 #> 06520019C0023R      0.6139914      0.6389785      0.8583166      0.8280060 #>                06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> 06520011B0023R      0.6633748      0.9079581      0.8818454      0.9117386 #> 06520067C0018R      0.6604377      0.8775734      0.8570700      0.9142934 #> 06520063C0043R      0.6113716      0.5978126      0.6658466      0.8104461 #> 06520105C0017R      0.4520703      0.4172803      0.5111085      0.6131335 #> 06520092C0017R      1.0000000      0.7033489      0.6871754      0.7101840 #> 06520103C0017R      0.7033489      1.0000000      0.9863276      0.9000953 #> 06520001B0023R      0.6871754      0.9863276      1.0000000      0.9227436 #> 06520022C0017R      0.7101840      0.9000953      0.9227436      1.0000000 #> 06520062C0017R      0.5895186      0.5725651      0.6362937      0.8010688 #> 06520046C0018R      0.2638231      0.1279450      0.1317451      0.3080865 #> 06520101B0017R      0.7254041      0.9743803      0.9576231      0.9137366 #> 06520047C0017R      0.5043505      0.5349226      0.5188468      0.6281087 #> 06520024B0014R      0.4709462      0.4768380      0.5041802      0.6294704 #> 06520080B0023R      0.5609389      0.4894940      0.5836644      0.7307929 #> 06520093C0017R      0.6241234      0.4080609      0.4799501      0.6398497 #> 06520070C0018R      0.5547028      0.5587841      0.6561649      0.7291685 #> 06520023C0018R      0.5100178      0.4636074      0.5662647      0.6677198 #> 06520099B0017R      0.5000248      0.3018044      0.3613744      0.5875554 #> 06520015C0016R      0.6949487      0.9262604      0.9682275      0.9302252 #> 06520019C0023R      0.6235283      0.6475062      0.7162892      0.8016153 #>                06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> 06520011B0023R      0.6753364      0.3208473      0.9314543      0.6815391 #> 06520067C0018R      0.7157011      0.3148823      0.9041533      0.6707660 #> 06520063C0043R      0.8896542      0.4431801      0.6417565      0.5759576 #> 06520105C0017R      0.7652040      0.3814626      0.4319133      0.4652142 #> 06520092C0017R      0.5895186      0.2638231      0.7254041      0.5043505 #> 06520103C0017R      0.5725651      0.1279450      0.9743803      0.5349226 #> 06520001B0023R      0.6362937      0.1317451      0.9576231      0.5188468 #> 06520022C0017R      0.8010688      0.3080865      0.9137366      0.6281087 #> 06520062C0017R      1.0000000      0.4747608      0.6236545      0.6631752 #> 06520046C0018R      0.4747608      1.0000000      0.2381617      0.7655772 #> 06520101B0017R      0.6236545      0.2381617      1.0000000      0.6128255 #> 06520047C0017R      0.6631752      0.7655772      0.6128255      1.0000000 #> 06520024B0014R      0.6813321      0.4423075      0.5302252      0.5880107 #> 06520080B0023R      0.8997510      0.4212484      0.5343559      0.5282159 #> 06520093C0017R      0.7530101      0.3954200      0.5019182      0.4276193 #> 06520070C0018R      0.8248334      0.3424986      0.5564180      0.4850496 #> 06520023C0018R      0.8045479      0.4105629      0.4729066      0.5008448 #> 06520099B0017R      0.7839665      0.5424584      0.4246231      0.5237444 #> 06520015C0016R      0.7306067      0.1605127      0.8992993      0.5037995 #> 06520019C0023R      0.8610609      0.4903751      0.6754787      0.6867600 #>                06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> 06520011B0023R      0.5835149      0.5168947      0.4138013      0.4697837 #> 06520067C0018R      0.5819907      0.5524994      0.4497814      0.5046432 #> 06520063C0043R      0.6588440      0.8949026      0.7953623      0.8295754 #> 06520105C0017R      0.5231136      0.8217901      0.7202175      0.8553639 #> 06520092C0017R      0.4709462      0.5609389      0.6241234      0.5547028 #> 06520103C0017R      0.4768380      0.4894940      0.4080609      0.5587841 #> 06520001B0023R      0.5041802      0.5836644      0.4799501      0.6561649 #> 06520022C0017R      0.6294704      0.7307929      0.6398497      0.7291685 #> 06520062C0017R      0.6813321      0.8997510      0.7530101      0.8248334 #> 06520046C0018R      0.4423075      0.4212484      0.3954200      0.3424986 #> 06520101B0017R      0.5302252      0.5343559      0.5019182      0.5564180 #> 06520047C0017R      0.5880107      0.5282159      0.4276193      0.4850496 #> 06520024B0014R      1.0000000      0.6059874      0.5317071      0.5407754 #> 06520080B0023R      0.6059874      1.0000000      0.8384252      0.8961184 #> 06520093C0017R      0.5317071      0.8384252      1.0000000      0.7933036 #> 06520070C0018R      0.5407754      0.8961184      0.7933036      1.0000000 #> 06520023C0018R      0.5403914      0.8941102      0.8082247      0.9658703 #> 06520099B0017R      0.5677268      0.8092670      0.8884675      0.6897805 #> 06520015C0016R      0.5410291      0.7177895      0.6165727      0.8088963 #> 06520019C0023R      0.6251164      0.8780061      0.7894097      0.9381035 #>                06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> 06520011B0023R      0.4033409      0.4224672      0.8093514      0.6139914 #> 06520067C0018R      0.4404680      0.4766716      0.8036729      0.6389785 #> 06520063C0043R      0.8266231      0.7936238      0.7640655      0.8583166 #> 06520105C0017R      0.8575140      0.6681055      0.6482306      0.8280060 #> 06520092C0017R      0.5100178      0.5000248      0.6949487      0.6235283 #> 06520103C0017R      0.4636074      0.3018044      0.9262604      0.6475062 #> 06520001B0023R      0.5662647      0.3613744      0.9682275      0.7162892 #> 06520022C0017R      0.6677198      0.5875554      0.9302252      0.8016153 #> 06520062C0017R      0.8045479      0.7839665      0.7306067      0.8610609 #> 06520046C0018R      0.4105629      0.5424584      0.1605127      0.4903751 #> 06520101B0017R      0.4729066      0.4246231      0.8992993      0.6754787 #> 06520047C0017R      0.5008448      0.5237444      0.5037995      0.6867600 #> 06520024B0014R      0.5403914      0.5677268      0.5410291      0.6251164 #> 06520080B0023R      0.8941102      0.8092670      0.7177895      0.8780061 #> 06520093C0017R      0.8082247      0.8884675      0.6165727      0.7894097 #> 06520070C0018R      0.9658703      0.6897805      0.8088963      0.9381035 #> 06520023C0018R      1.0000000      0.7296291      0.7286448      0.9323267 #> 06520099B0017R      0.7296291      1.0000000      0.4846711      0.7380609 #> 06520015C0016R      0.7286448      0.4846711      1.0000000      0.8240416 #> 06520019C0023R      0.9323267      0.7380609      0.8240416      1.0000000 #> Slot \"flag_data\": #> DataFrame with 20 rows and 2 columns #>                tech_failure_flag low_depth_flag #>                        <logical>      <logical> #> 06520011B0023R             FALSE          FALSE #> 06520067C0018R             FALSE          FALSE #> 06520063C0043R             FALSE           TRUE #> 06520105C0017R             FALSE          FALSE #> 06520092C0017R             FALSE          FALSE #> ...                          ...            ... #> 06520070C0018R             FALSE          FALSE #> 06520023C0018R             FALSE          FALSE #> 06520099B0017R             FALSE          FALSE #> 06520015C0016R             FALSE          FALSE #> 06520019C0023R             FALSE          FALSE #>   # We can specify another correlation coefficient to be calculated. result <- correlate(object, method = \"spearman\")  # Plot the correlation matrix. autoplot(result)   # We can customize the heatmap. autoplot(result, show_column_names = FALSE, show_row_names = FALSE)   # Including changing the axis label text size. autoplot(   result,   row_names_gp = grid::gpar(fontsize = 8),   column_names_gp = grid::gpar(fontsize = 8) )"},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Principal Components Analysis Calculation — calc_pca","title":"Principal Components Analysis Calculation — calc_pca","text":"calc_pca() function performs principal components analysis gene count vectors across samples. corresponding autoplot() method can visualize results.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Principal Components Analysis Calculation — calc_pca","text":"","code":"calc_pca(object, assay_name = \"counts\", n_top = NULL)"},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Principal Components Analysis Calculation — calc_pca","text":"object (AnyHermesData)  input. assay_name (string)  name assay use. n_top (count NULL) filter criteria based number genes maximum variance.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Principal Components Analysis Calculation — calc_pca","text":"HermesDataPca object extension stats::prcomp class.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Principal Components Analysis Calculation — calc_pca","text":"PCA performed filtering low quality genes samples, well normalization counts. addition, genes constant counts across samples excluded analysis internally calc_pca(). Centering scaling also applied internally. Plots can obtained ggplot2::autoplot() function corresponding method ggfortify package plot results principal components analysis saved HermesDataPca object. See ggfortify::autoplot.prcomp() details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/calc_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Principal Components Analysis Calculation — calc_pca","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  result <- calc_pca(object, assay_name = \"tpm\") summary(result) #> Importance of first k=18 (out of 19) components: #>                            PC1     PC2     PC3      PC4      PC5     PC6 #> Standard deviation     22.9971 18.7315 16.3042 13.47009 13.05843 11.4881 #> Proportion of Variance  0.2212  0.1467  0.1112  0.07589  0.07132  0.0552 #> Cumulative Proportion   0.2212  0.3679  0.4791  0.55500  0.62632  0.6815 #>                             PC7     PC8     PC9    PC10    PC11    PC12    PC13 #> Standard deviation     10.60653 9.67291 9.29607 8.97324 8.54474 8.11786 7.70847 #> Proportion of Variance  0.04705 0.03913 0.03614 0.03368 0.03054 0.02756 0.02485 #> Cumulative Proportion   0.72857 0.76770 0.80384 0.83752 0.86805 0.89562 0.92047 #>                           PC14    PC15    PC16    PC17    PC18 #> Standard deviation     7.20798 6.91976 6.11309 5.77360 4.42960 #> Proportion of Variance 0.02173 0.02003 0.01563 0.01394 0.00821 #> Cumulative Proportion  0.94220 0.96222 0.97785 0.99179 1.00000  result1 <- calc_pca(object, assay_name = \"tpm\", n_top = 500) summary(result1) #> Importance of first k=18 (out of 19) components: #>                            PC1    PC2     PC3     PC4     PC5     PC6     PC7 #> Standard deviation     11.2652 9.6518 6.89353 6.34548 5.29254 5.20812 4.70857 #> Proportion of Variance  0.2538 0.1863 0.09504 0.08053 0.05602 0.05425 0.04434 #> Cumulative Proportion   0.2538 0.4401 0.53517 0.61570 0.67172 0.72597 0.77031 #>                           PC8     PC9   PC10    PC11   PC12    PC13    PC14 #> Standard deviation     4.2012 4.06409 3.7884 3.51647 3.2405 3.07753 3.04570 #> Proportion of Variance 0.0353 0.03303 0.0287 0.02473 0.0210 0.01894 0.01855 #> Cumulative Proportion  0.8056 0.83864 0.8673 0.89208 0.9131 0.93202 0.95058 #>                           PC15    PC16    PC17    PC18 #> Standard deviation     2.87077 2.65226 2.46289 1.83598 #> Proportion of Variance 0.01648 0.01407 0.01213 0.00674 #> Cumulative Proportion  0.96706 0.98113 0.99326 1.00000  # Plot the results. autoplot(result)  autoplot(result, x = 2, y = 3)  autoplot(result, variance_percentage = FALSE)  autoplot(result, label = TRUE, label.repel = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/reference/cat_with_newline.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate and Print with Newline — cat_with_newline","title":"Concatenate and Print with Newline — cat_with_newline","text":"function concatenates inputs like cat() prints newline.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cat_with_newline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate and Print with Newline — cat_with_newline","text":"","code":"cat_with_newline(...)"},{"path":"https://insightsengineering.github.io/hermes/reference/cat_with_newline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate and Print with Newline — cat_with_newline","text":"... inputs concatenate.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cat_with_newline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate and Print with Newline — cat_with_newline","text":"None, used side effect producing concatenated output R console.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/cat_with_newline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Concatenate and Print with Newline — cat_with_newline","text":"","code":"cat_with_newline(\"hello\", \"world\") #> hello world"},{"path":"https://insightsengineering.github.io/hermes/reference/cbind.html","id":null,"dir":"Reference","previous_headings":"","what":"Column Binding of AnyHermesData Objects — cbind","title":"Column Binding of AnyHermesData Objects — cbind","text":"method combines AnyHermesData objects ranges different samples (columns assays).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cbind.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column Binding of AnyHermesData Objects — cbind","text":"... (AnyHermesData) objects column bind.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cbind.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Column Binding of AnyHermesData Objects — cbind","text":"combined AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cbind.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Column Binding of AnyHermesData Objects — cbind","text":"Note just inherits SummarizedExperiment::cbind,SummarizedExperiment-method(). binding AnyHermesData object SummarizedExperiment::SummarizedExperiment object, result SummarizedExperiment::SummarizedExperiment object (general class). Note combined object needs unique sample IDs (column names).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/cbind.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Column Binding of AnyHermesData Objects — cbind","text":"","code":"a <- hermes_data[, 1:10] b <- hermes_data[, 11:20] result <- cbind(a, b) class(result) #> [1] \"HermesData\" #> attr(,\"package\") #> [1] \"hermes\""},{"path":"https://insightsengineering.github.io/hermes/reference/check_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for proportion — check_proportion","title":"Check for proportion — check_proportion","text":"Check whether x (single) proportion.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/check_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for proportion — check_proportion","text":"","code":"check_proportion(x, null.ok = FALSE)  assert_proportion(   x,   null.ok = FALSE,   .var.name = checkmate::vname(x),   add = NULL )  test_proportion(x, null.ok = FALSE)  expect_proportion(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/hermes/reference/check_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for proportion — check_proportion","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/check_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check for proportion — check_proportion","text":"TRUE successful, otherwise string error message.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/check_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for proportion — check_proportion","text":"","code":"check_proportion(0.25) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/hermes/reference/colMeanZscores.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean Z-score Gene Signature — colMeanZscores","title":"Mean Z-score Gene Signature — colMeanZscores","text":"helper function returns Z-score assay stored matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colMeanZscores.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean Z-score Gene Signature — colMeanZscores","text":"","code":"colMeanZscores(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/colMeanZscores.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean Z-score Gene Signature — colMeanZscores","text":"x (matrix) containing numeric data genes rows samples columns, missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colMeanZscores.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean Z-score Gene Signature — colMeanZscores","text":"numeric vector containing mean Z-score values column x.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colMeanZscores.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean Z-score Gene Signature — colMeanZscores","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize() %>%   assay(\"counts\")  colMeanZscores(object) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>   5.195107e-04  -1.189550e-03   1.155081e-04   3.308070e-04  -1.130575e-03  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520101B0017R  #>   1.688234e-03   5.201127e-05  -1.145377e-03   1.922514e-03  -1.779591e-03  #> 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R  #>   2.320730e-04  -4.893309e-04   9.562463e-04  -3.677371e-04  -9.567040e-04  #> 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>  -5.682047e-04   7.648360e-04   2.441182e-04   8.012106e-04"},{"path":"https://insightsengineering.github.io/hermes/reference/colPrinComp1.html","id":null,"dir":"Reference","previous_headings":"","what":"First Principal Component (PC1) Gene Signature — colPrinComp1","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"helper function returns first principal component assay stored matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colPrinComp1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"","code":"colPrinComp1(x, center = TRUE, scale = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/reference/colPrinComp1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"x (matrix) containing numeric data genes rows samples columns, missing values allowed. center (flag) whether variables zero centered. scale (flag) whether variables scaled unit variance.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colPrinComp1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"numeric vector containing principal component values column x.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/colPrinComp1.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"First Principal Component (PC1) Gene Signature — colPrinComp1","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize() %>%   assay(\"counts\")  colPrinComp1(object) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>    -22.7211514    -16.5888471     -8.6643020    -20.3183592     13.4998779  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520101B0017R  #>     17.9491775      4.7633163    -10.6928704    -16.1907212     30.3749930  #> 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R  #>    -25.6029134    -18.1914202     -6.9932017     36.8659028      0.7099287  #> 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>     -5.3048871     32.7696234      9.9885728      4.3472814"},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample Variables with Selected Gene Information — col_data_with_genes","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"obtains sample variables HermesData object together selected gene information.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"","code":"col_data_with_genes(object, assay_name, genes)"},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"object (AnyHermesData) input experiment. assay_name (string) assay use. genes (GeneSpec) genes gene signature extracted.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"combined data set, additional attribute gene_cols contains names columns obtained extracting genes information.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"class returned data set depend class colData, usually S4Vectors::DFrame.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/col_data_with_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample Variables with Selected Gene Information — col_data_with_genes","text":"","code":"result <- col_data_with_genes(hermes_data, \"counts\", gene_spec(\"GeneID:1820\")) tail(names(result)) #> [1] \"COHORT\"            \"TTYPE\"             \"STDSSDY\"           #> [4] \"low_depth_flag\"    \"tech_failure_flag\" \"GeneID.1820\"       result$GeneID.1820 #>  [1]  49 153  94  54 111 567 118 171 180  16 386  57 242  73 362 144 124 243  79 #> [20] 161"},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Connection to BioMart — connect_biomart","title":"Connection to BioMart — connect_biomart","text":"connect_biomart() creates connection object class ConnectionBiomart contains biomaRt object class biomaRt::Mart prefix object used downstream query.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Connection to BioMart — connect_biomart","text":"","code":"connect_biomart(prefix = c(\"ENSG\", \"GeneID\"), version = NULL)"},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connection to BioMart — connect_biomart","text":"prefix (string) gene ID prefix. version (string NULL) optional Ensembl version use. NULL latest available release used.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Connection to BioMart — connect_biomart","text":"ConnectionBiomart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Connection to BioMart — connect_biomart","text":"connects Ensembl data base BioMart human genes. specific version can optionally chosen ensure reproducibility results new release available, accessed data might change.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/connect_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Connection to BioMart — connect_biomart","text":"","code":"if (interactive()) {   connection <- connect_biomart(\"ENSG\") }"},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Control Settings for Counts Normalization — control_normalize","title":"Control Settings for Counts Normalization — control_normalize","text":"control function allows easy customization normalization settings.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control Settings for Counts Normalization — control_normalize","text":"","code":"control_normalize(   log = TRUE,   lib_sizes = NULL,   prior_count = 1,   fit_type = \"parametric\" )"},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control Settings for Counts Normalization — control_normalize","text":"log (flag) whether log2 values returned, otherwise original scale used. lib_sizes (NULL counts) library sizes, NULL vector sum counts samples used. prior_count (non-negative number) average count added observation avoid taking log zero, used log = TRUE. fit_type (string) method estimate dispersion parameters Negative Binomial model, used normalize() methods include vst /rlog. See estimateDispersions details.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control Settings for Counts Normalization — control_normalize","text":"List settings used perform normalization procedure.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Control Settings for Counts Normalization — control_normalize","text":"used normalize() function.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control Settings for Counts Normalization — control_normalize","text":"","code":"control_normalize() #> $log #> [1] TRUE #>  #> $lib_sizes #> NULL #>  #> $prior_count #> [1] 1 #>  #> $fit_type #> [1] \"parametric\" #>  control_normalize(log = FALSE, lib_sizes = rep(1e6L, 20)) #> $log #> [1] FALSE #>  #> $lib_sizes #>  [1] 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 #> [10] 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 1000000 #> [19] 1000000 1000000 #>  #> $prior_count #> [1] 1 #>  #> $fit_type #> [1] \"parametric\" #>"},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Control for Specified Quality Flags — control_quality","title":"Control for Specified Quality Flags — control_quality","text":"Control function specifies quality flag settings. One settings can customized. specified settings left defaults.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control for Specified Quality Flags — control_quality","text":"","code":"control_quality(   min_cpm = 1,   min_cpm_prop = 0.25,   min_corr = 0.5,   min_depth = NULL )"},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control for Specified Quality Flags — control_quality","text":"min_cpm (non-negative number) minimum Counts per Million (CPM) gene within sample. min_cpm_prop (proportion) minimum proportion samples acceptable CPM certain gene low expression flagging. min_corr (proportion) minimum Pearson correlation coefficient CPM samples technical failure flagging. min_depth (non-negative count NULL) minimum library depth low depth flagging. NULL, calculated first quartile minus 1.5 times inter-quartile range library size (depth) samples. (anything usual lower boxplot whisker low.)","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control for Specified Quality Flags — control_quality","text":"List criteria flag observations.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Control for Specified Quality Flags — control_quality","text":"used add_quality_flags() function.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/control_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control for Specified Quality Flags — control_quality","text":"","code":"# Default settings. control_quality() #> $min_cpm #> [1] 1 #>  #> $min_cpm_prop #> [1] 0.25 #>  #> $min_corr #> [1] 0.5 #>  #> $min_depth #> NULL #>   # One or more settings can be customized. control_quality(min_cpm = 5, min_cpm_prop = 0.001) #> $min_cpm #> [1] 5 #>  #> $min_cpm_prop #> [1] 0.001 #>  #> $min_corr #> [1] 0.5 #>  #> $min_depth #> NULL #>"},{"path":"https://insightsengineering.github.io/hermes/reference/correlate.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic Function for Correlation Calculations — correlate","title":"Generic Function for Correlation Calculations — correlate","text":"New generic function calculate correlations one two objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/correlate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic Function for Correlation Calculations — correlate","text":"","code":"correlate(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/correlate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic Function for Correlation Calculations — correlate","text":"object input class used decide method. ... additional arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/correlate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generic Function for Correlation Calculations — correlate","text":"Corresponding object contains correlation results.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/correlate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generic Function for Correlation Calculations — correlate","text":"","code":"sample_cors <- correlate(hermes_data) autoplot(sample_cors)   pca_sample_var_cors <- correlate(calc_pca(hermes_data), hermes_data) autoplot(pca_sample_var_cors)"},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts Accessor and Setter — counts,AnyHermesData-method","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"methods access set counts assay AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' counts(object, ...)  # S4 method for class 'AnyHermesData,matrix' counts(object, ..., withDimnames = TRUE) <- value"},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"object (AnyHermesData) object access counts . ... used. withDimnames (flag) setting withDimnames =FALSE setter (counts<-) required dimnames supplied counts assay identical dimnames AnyHermesData object; influence actual assignment dimnames assay (always stored -). value (matrix) counts assay replaced .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"counts assay.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"counts(object = AnyHermesData) <- value:","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Counts Accessor and Setter — counts,AnyHermesData-method","text":"","code":"a <- hermes_data result <- counts(a) class(result) #> [1] \"matrix\" \"array\"  head(result) #>                  06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:11185                  3             66             35             10 #> GeneID:10677               1668            236             95           1945 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                113             11            153             22 #>                  06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> GeneID:11185                 68            123             65             10 #> GeneID:10677                570            149            216            182 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                  0             20              1              5 #>                  06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> GeneID:11185                106             23             72              4 #> GeneID:10677                138            748            314            189 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                131            586              0            119 #>                  06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> GeneID:11185                 36              0             50            479 #> GeneID:10677                176            213            313            345 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881                  9             62              0            482 #>                  06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> GeneID:11185                235             35             75             47 #> GeneID:10677               1922            269            385            687 #> GeneID:101928428              0              0              0              0 #> GeneID:100422835              0              0              0              0 #> GeneID:102466731              0              0              0              0 #> GeneID:64881               1315              0           3047            135 counts(a) <- counts(a) + 100L head(counts(a)) #>                  06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R #> GeneID:11185                103            166            135            110 #> GeneID:10677               1768            336            195           2045 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                213            111            253            122 #>                  06520092C0017R 06520103C0017R 06520001B0023R 06520022C0017R #> GeneID:11185                168            223            165            110 #> GeneID:10677                670            249            316            282 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                100            120            101            105 #>                  06520062C0017R 06520046C0018R 06520101B0017R 06520047C0017R #> GeneID:11185                206            123            172            104 #> GeneID:10677                238            848            414            289 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                231            686            100            219 #>                  06520024B0014R 06520080B0023R 06520093C0017R 06520070C0018R #> GeneID:11185                136            100            150            579 #> GeneID:10677                276            313            413            445 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881                109            162            100            582 #>                  06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R #> GeneID:11185                335            135            175            147 #> GeneID:10677               2022            369            485            787 #> GeneID:101928428            100            100            100            100 #> GeneID:100422835            100            100            100            100 #> GeneID:102466731            100            100            100            100 #> GeneID:64881               1415            100           3147            235"},{"path":"https://insightsengineering.github.io/hermes/reference/cut_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"function transforms numeric vector factor corresponding quantile intervals. intervals left-open right-closed.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cut_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"","code":"cut_quantile(x, percentiles = c(1/3, 2/3), digits = 0)"},{"path":"https://insightsengineering.github.io/hermes/reference/cut_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"x (numeric) continuous variable values cut quantile bins. NA values taken account computing quantiles attributed NA interval. percentiles (proportions) required percentiles quantile intervals generated. Duplicated values removed. digits (integer)  precision use formatting percentages.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cut_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"factor description available quantiles levels.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/cut_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cutting a Numeric Vector into a Factor of Quantile Bins — cut_quantile","text":"","code":"set.seed(452) x <- runif(10, -10, 10) cut_quantile(x, c(0.33333333, 0.6666666), digits = 4) #>  [1] [0%,33.3333%]       (33.3333%,66.6667%] [0%,33.3333%]       #>  [4] (66.6667%,100%]     (33.3333%,66.6667%] [0%,33.3333%]       #>  [7] (66.6667%,100%]     (33.3333%,66.6667%] (33.3333%,66.6667%] #> [10] (66.6667%,100%]     #> Levels: [0%,33.3333%] (33.3333%,66.6667%] (66.6667%,100%]  x[1:4] <- NA cut_quantile(x) #>  [1] <NA>       <NA>       <NA>       <NA>       (33%,67%]  [0%,33%]   #>  [7] (67%,100%] (33%,67%]  [0%,33%]   (67%,100%] #> Levels: [0%,33%] (33%,67%] (67%,100%]"},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"utility function converts eligible character logical variables S4Vectors::DataFrame factor variables. factor variables get amended explicit missing level. includes NA empty strings.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"","code":"df_cols_to_factor(data, omit_columns = NULL, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"data (DataFrame) input S4Vectors::DataFrame. omit_columns (character NULL) columns omitted possible conversion factor explicit missing level application. na_level (string) explicit missing level used factor variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"modified data.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"required rowData colData variables converted ensure proper downstream behavior. automatically omitted found data therefore need specified omit_columns.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/df_cols_to_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of Eligible Columns to Factor Variables in a DataFrame — df_cols_to_factor","text":"","code":"dat <- colData(summarized_experiment) any(vapply(dat, is.character, logical(1))) #> [1] TRUE any(vapply(dat, is.logical, logical(1))) #> [1] TRUE dat_converted <- df_cols_to_factor(dat) any(vapply(dat_converted, function(x) is.character(x) || is.logical(x), logical(1))) #> [1] FALSE"},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential Expression Analysis — diff_expression","title":"Differential Expression Analysis — diff_expression","text":"diff_expression() function performs differential expression analysis using method preference. corresponding autoplot() method visualizing results volcano plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential Expression Analysis — diff_expression","text":"","code":"diff_expression(object, group, method = c(\"voom\", \"deseq2\"), ...)  # S4 method for class 'HermesDataDiffExpr' autoplot(object, adj_p_val_thresh = 0.05, log2_fc_thresh = 2.5)"},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential Expression Analysis — diff_expression","text":"object (AnyHermesData) input. Note function uses original counts analysis, need normalized. group (string) name factor variable 2 levels colData(object). 2 levels compared differential expression analysis. method (string) method differential expression analysis, see details . ... additional arguments passed helper function associated selected method. adj_p_val_thresh (proportion) threshold adjusted p-values (y-axis) flag significance. log2_fc_thresh (number) threshold absolute log2 fold-change (x-axis) flag - -regulation transcription.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential Expression Analysis — diff_expression","text":"HermesDataDiffExpr object data frame following columns gene HermesData object: log2_fc (estimate log2 fold change 2 levels provided factor) stat (test statistic, one depends method used) p_val (raw p-value) adj_p_val (multiplicity adjusted p-value value)","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Differential Expression Analysis — diff_expression","text":"Possible method choices : voom: uses limma::voom(), see h_diff_expr_voom() details. deseq2: uses DESeq2::DESeq(), see h_diff_expr_deseq2() details.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Differential Expression Analysis — diff_expression","text":"autoplot(HermesDataDiffExpr): generates volcano plot HermesDataDiffExpr object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Differential Expression Analysis — diff_expression","text":"provide df_cols_to_factor() utility function makes easy convert colData() character logical variables factors, can subsequently used group inputs. See example. order avoid warning using deseq2, can necessary specify fitType = \"local\" additional argument. e.g. case samples present case default parametric dispersions estimation work.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/diff_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Differential Expression Analysis — diff_expression","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter()  # Convert character and logical to factor variables in `colData`, # including the below used `group` variable. colData(object) <- df_cols_to_factor(colData(object)) res1 <- diff_expression(object, group = \"SEX\", method = \"voom\") head(res1) #>                  log2_fc      stat       p_val adj_p_val #> GeneID:344558  1.4951365  3.768257 0.001217934 0.7815544 #> GeneID:51227  -1.0670584 -3.766113 0.001224023 0.7815544 #> GeneID:10280  -0.7518694 -3.461800 0.002478362 0.7815544 #> GeneID:9435    1.8555120  3.414364 0.002764727 0.7815544 #> GeneID:51575  -0.7238103 -3.326330 0.003384750 0.7815544 #> GeneID:123036  2.8900474  3.246333 0.004064925 0.7815544 res2 <- diff_expression(object, group = \"SEX\", method = \"deseq2\") head(res2) #>                  log2_fc      stat        p_val   adj_p_val #> GeneID:64344  -2.9129064 -4.864176 1.149347e-06 0.002694069 #> GeneID:9002    2.3092323  4.215740 2.489604e-05 0.020061145 #> GeneID:167681 -4.0974632 -4.201788 2.648146e-05 0.020061145 #> GeneID:51227  -1.1573425 -4.143302 3.423404e-05 0.020061145 #> GeneID:4359    2.8926465  4.004010 6.227765e-05 0.029195764 #> GeneID:10280  -0.7997803 -3.876433 1.059991e-04 0.031057749  # Pass method arguments to the internally used helper functions. res3 <- diff_expression(object, group = \"SEX\", method = \"voom\", robust = TRUE, trend = TRUE) head(res3) #>                  log2_fc      stat       p_val adj_p_val #> GeneID:51227  -1.0670584 -3.765145 0.001226726 0.7884829 #> GeneID:344558  1.4951365  3.759186 0.001243851 0.7884829 #> GeneID:10280  -0.7518694 -3.467915 0.002443545 0.7884829 #> GeneID:9435    1.8555120  3.390300 0.002922073 0.7884829 #> GeneID:51575  -0.7238103 -3.325713 0.003389426 0.7884829 #> GeneID:123036  2.8900474  3.232786 0.004230256 0.7884829 res4 <- diff_expression(object, group = \"SEX\", method = \"deseq2\", fitType = \"local\") head(res4) #>                  log2_fc      stat        p_val   adj_p_val #> GeneID:64344  -2.9128847 -4.892128 9.975152e-07 0.002338176 #> GeneID:9002    2.3091854  4.256818 2.073572e-05 0.014702529 #> GeneID:167681 -4.0975071 -4.300519 1.703986e-05 0.014702529 #> GeneID:51227  -1.1573487 -4.213992 2.508964e-05 0.014702529 #> GeneID:4359    2.8925392  4.055798 4.996349e-05 0.021309899 #> GeneID:10280  -0.7997974 -3.958566 7.540117e-05 0.021309899  # Create the corresponding volcano plots. autoplot(res1)  autoplot(res3)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Barplot for Gene Expression Percentiles — draw_barplot","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"produces barplot dichotomized gene expression counts two three categories based custom defined percentiles.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"","code":"draw_barplot(   object,   assay_name,   x_spec,   facet_var = NULL,   fill_var = NULL,   percentiles = c(1/3, 2/3) )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input. x_spec (GeneSpec) gene specification x-axis. facet_var (string NULL) optional faceting variable, taken input sample variables. fill_var (string NULL) optional fill variable, taken input sample variables. percentiles (vector) lower upper percentiles dichotomize gene counts two three categories.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"ggplot barplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Barplot for Gene Expression Percentiles — draw_barplot","text":"","code":"object <- hermes_data  g <- genes(object)  draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1]),   facet_var = \"SEX\",   fill_var = \"AGE18\" )   draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1:3], colMedians, \"Median\"),   facet_var = \"SEX\",   fill_var = \"AGE18\" )   draw_barplot(   object,   assay_name = \"counts\",   x_spec = gene_spec(g[1:3], colMeans, \"Mean\"),   facet_var = \"SEX\",   fill_var = \"AGE18\",   percentiles = c(0.1, 0.9) )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Boxplot for Gene Expression Values — draw_boxplot","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"produces boxplots gene expression values single gene, multiple genes gene signature.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"","code":"draw_boxplot(   object,   assay_name,   genes,   x_var = NULL,   color_var = NULL,   facet_var = NULL,   violin = FALSE,   jitter = FALSE )  h_draw_boxplot_df(object, assay_name, genes, x_var, color_var, facet_var)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input y-axis. genes (GeneSpec) genes gene signature produce boxplots. x_var (string NULL) optional stratifying variable x-axis, taken input sample variables. color_var (string NULL) optional color variable, taken input sample variables. facet_var (string NULL) optional faceting variable, taken input sample variables. violin (flag) whether draw violin plot instead boxplot. jitter (flag) whether add jittered original data points.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"ggplot boxplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"h_draw_boxplot_df(): Helper function prepare data frame required plotting.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Boxplot for Gene Expression Values — draw_boxplot","text":"","code":"object <- hermes_data draw_boxplot(   object,   assay_name = \"counts\",   genes = gene_spec(c(A = genes(object)[1])),   violin = TRUE )   object2 <- object %>%   add_quality_flags() %>%   filter() %>%   normalize() draw_boxplot(   object2,   assay_name = \"tpm\",   x_var = \"SEX\",   genes = gene_spec(setNames(genes(object2)[1:10], 1:10), fun = colMeans),   facet_var = \"RACE\",   color_var = \"AGE18\",   jitter = TRUE )   draw_boxplot(   object,   assay_name = \"counts\",   x_var = \"SEX\",   genes = gene_spec(genes(object)[1:3]),   jitter = TRUE,   facet_var = \"AGE18\" )   draw_boxplot(   object,   assay_name = \"counts\",   genes = gene_spec(c(A = \"GeneID:11185\", B = \"GeneID:10677\")),   violin = TRUE )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_genes_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"creates barplot chromosomes AnyHermesData object proportions low expression genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_genes_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"","code":"draw_genes_barplot(   object,   chromosomes = c(seq_len(22), \"X\", \"Y\", \"MT\"),   include_others = TRUE )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_genes_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"object (AnyHermesData) input. chromosomes (character) names chromosomes displayed. include_others (flag) option show chromosomes chromosomes \"Others\".","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_genes_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"ggplot object histogram.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_genes_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stacked Barplot of Low Expression Genes by Chromosome — draw_genes_barplot","text":"","code":"object <- hermes_data  # Display chromosomes 1-22, X, Y, and MT. Other chromosomes are displayed in \"Others\". # To increase readability, we can have flip the coordinate axes. draw_genes_barplot(object) + coord_flip()   # Alternatively we can also rotate the x-axis tick labels. draw_genes_barplot(object) + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))   # Display chromosomes 1 and 2. Other chromosomes are displayed in \"Others\". draw_genes_barplot(object, chromosomes = c(\"1\", \"2\"))   # Display chromosomes 1 and 2 only. draw_genes_barplot(object, chromosomes = c(\"1\", \"2\"), include_others = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_heatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"Heatmap for Gene Expression Counts — draw_heatmap","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"produces heatmap chosen assay groups various sample variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_heatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"","code":"draw_heatmap(   object,   assay_name,   color_extremes = c(0.01, 0.99),   col_data_annotation = NULL,   ... )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_heatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"object (AnyHermesData) input. assay_name (string) selects assay input. color_extremes (numeric) min max percentiles inform color scheme heatmap blue red respectively. col_data_annotation (character NULL) optional grouping variable(s), taken input sample variables. ... additional arguments pass ComplexHeatmap::Heatmap().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_heatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"ComplexHeatmap::Heatmap heatmap","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_heatmap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Heatmap for Gene Expression Counts — draw_heatmap","text":"","code":"result <- hermes_data %>%   normalize(methods = \"voom\") %>%   add_quality_flags() %>%   filter(what = \"genes\")  draw_heatmap(   object = result[1:10, ],   assay_name = \"counts\",   col_data_annotation = \"COUNTRY\" )   draw_heatmap(   object = result[1:10, ],   assay_name = \"counts\",   color_extremes = c(0.001, 0.999),   col_data_annotation = \"AGEGRP\" )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_densities.html","id":null,"dir":"Reference","previous_headings":"","what":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"creates density plot (log) counts distributions AnyHermesData object line plot corresponds sample.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_densities.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"","code":"draw_libsize_densities(object, log = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_densities.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"object (AnyHermesData) input. log (flag) counts log transformed (log2).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_densities.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"ggplot object density plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_densities.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density Plot of (Log) Counts Distributions — draw_libsize_densities","text":"","code":"result <- hermes_data draw_libsize_densities(result)  draw_libsize_densities(result, log = FALSE)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_hist.html","id":null,"dir":"Reference","previous_headings":"","what":"Histogram of Library Sizes — draw_libsize_hist","title":"Histogram of Library Sizes — draw_libsize_hist","text":"creates histogram library sizes AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_hist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Histogram of Library Sizes — draw_libsize_hist","text":"","code":"draw_libsize_hist(object, bins = 30L, fill = \"darkgrey\")"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_hist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Histogram of Library Sizes — draw_libsize_hist","text":"object (AnyHermesData) input. bins (count) number evenly distributed groups desired. fill (string) color bars filling.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_hist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Histogram of Library Sizes — draw_libsize_hist","text":"ggplot object histogram.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_hist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Histogram of Library Sizes — draw_libsize_hist","text":"","code":"result <- hermes_data draw_libsize_hist(result)  draw_libsize_hist(result, bins = 10L, fill = \"blue\")"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_qq.html","id":null,"dir":"Reference","previous_headings":"","what":"Q-Q Plot of Library Sizes — draw_libsize_qq","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"creates Q-Q plot library sizes AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_qq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"","code":"draw_libsize_qq(object, color = \"grey\", linetype = \"dashed\")"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_qq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"object (AnyHermesData) input. color (string) color Q-Q line. linetype (string) line type  Q-Q line.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_qq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"ggplot object Q-Q Plot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_libsize_qq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Q-Q Plot of Library Sizes — draw_libsize_qq","text":"","code":"result <- hermes_data draw_libsize_qq(result)  draw_libsize_qq(result, color = \"blue\", linetype = \"solid\")   # We can also add sample names as labels. library(ggrepel) draw_libsize_qq(result) + geom_text_repel(label = colnames(result), stat = \"qq\")"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_nonzero_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"draws boxplot, overlaid data points, number non-zero expressed genes per sample.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_nonzero_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"","code":"draw_nonzero_boxplot(object, position = position_jitter(0.2), alpha = 0.25)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_nonzero_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"object (AnyHermesData) input. position (Position) specifies x-axis position points, e.g. jittering. alpha (proportion) specifies transparency points.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_nonzero_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"ggplot object boxplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_nonzero_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Boxplot of Non-Zero Genes — draw_nonzero_boxplot","text":"","code":"# Default boxplot. result <- hermes_data draw_nonzero_boxplot(result)   # Reusing the same position for labeling. library(ggrepel) pos <- position_jitter(0.5) draw_nonzero_boxplot(result, position = pos) +   geom_text_repel(aes(label = samples(result)), position = pos)"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Scatterplot for Gene Expression Values — draw_scatterplot","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"produces scatterplot two genes gene signatures.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"","code":"draw_scatterplot(   object,   assay_name,   x_spec,   y_spec,   color_var = NULL,   facet_var = NULL,   smooth_method = c(\"lm\", \"loess\", \"none\") )"},{"path":"https://insightsengineering.github.io/hermes/reference/draw_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"object (AnyHermesData) input. assay_name (string) selects assay input. x_spec (GeneSpec) gene specification x-axis. y_spec (GeneSpec) gene specification y-axis. color_var (string NULL) optional color variable, taken input sample variables. facet_var (string NULL) optional faceting variable, taken input sample variables. smooth_method (string) smoothing method use, either linear regression line (lm), local polynomial regression (loess) none.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"ggplot scatterplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/draw_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Scatterplot for Gene Expression Values — draw_scatterplot","text":"","code":"object <- hermes_data g <- genes(object)  draw_scatterplot(   object,   assay_name = \"counts\",   facet_var = NULL,   x_spec = gene_spec(c(A = g[1])),   y_spec = gene_spec(g[2]),   color = \"RACE\" )   object2 <- object %>%   add_quality_flags() %>%   filter() %>%   normalize() g2 <- genes(object2)  draw_scatterplot(   object2,   assay_name = \"tpm\",   facet_var = \"SEX\",   x_spec = gene_spec(g2[1:10], colMeans, \"Mean\"),   y_spec = gene_spec(g2[11:20], colMedians, \"Median\"),   smooth_method = \"loess\" )"},{"path":"https://insightsengineering.github.io/hermes/reference/expression_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Example ExpressionSet Data — expression_set","title":"Example ExpressionSet Data — expression_set","text":"example data can used try conversion Biobase::ExpressionSet object HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/expression_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example ExpressionSet Data — expression_set","text":"","code":"expression_set"},{"path":"https://insightsengineering.github.io/hermes/reference/expression_set.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example ExpressionSet Data — expression_set","text":"Biobase::ExpressionSet object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/expression_set.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example ExpressionSet Data — expression_set","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/extra_data_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Extra Variable Names Accessor Methods — extra_data_names","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"methods access names variables colData() rowData() object required design. can additional sample patient characteristics, gene characteristics.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/extra_data_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"","code":"extraColDataNames(x, ...)  # S4 method for class 'AnyHermesData' extraColDataNames(x, ...)  extraRowDataNames(x, ...)  # S4 method for class 'AnyHermesData' extraRowDataNames(x, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/extra_data_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"x (AnyHermesData) object. ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/extra_data_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"character vector additional variable names either colData() rowData().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/extra_data_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extra Variable Names Accessor Methods — extra_data_names","text":"","code":"object <- hermes_data extraColDataNames(object) #>  [1] \"Filename\" \"SampleID\" \"AGEGRP\"   \"AGE18\"    \"STDDRS\"   \"STDDRSD\"  #>  [7] \"STDSSDT\"  \"TRTDRS\"   \"TRTDRSD\"  \"BHDCIRC\"  \"BHDCIRCU\" \"ADAFL\"    #> [13] \"BLANP\"    \"BKPS\"     \"BLKS\"     \"BTANNER\"  \"FRPST\"    \"DURIDX\"   #> [19] \"DURSAF\"   \"DURSUR\"   \"LNTHRPY\"  \"AENCIFL\"  \"STUDYID\"  \"USUBJID\"  #> [25] \"RFSTDTC\"  \"RFENDTC\"  \"RFXSTDTC\" \"RFXENDTC\" \"RFICDTC\"  \"RFPENDTC\" #> [31] \"DTHDTC\"   \"DTHFL\"    \"SITEID\"   \"INVID\"    \"AGE\"      \"AGEU\"     #> [37] \"SEX\"      \"RACE\"     \"ETHNIC\"   \"ARMCD\"    \"ARM\"      \"ACTARMCD\" #> [43] \"ACTARM\"   \"COUNTRY\"  \"DMDTC\"    \"DMDY\"     \"BAGE\"     \"BAGEU\"    #> [49] \"BWT\"      \"BWTU\"     \"BHT\"      \"BHTU\"     \"BBMI\"     \"ITTFL\"    #> [55] \"SAFFL\"    \"INFCODT\"  \"RANDDT\"   \"TRTSDTC\"  \"TRTSDTM\"  \"TRTSTMF\"  #> [61] \"TRTEDTM\"  \"TRTETMF\"  \"TRTDUR\"   \"DISCSTUD\" \"DISCDEAT\" \"DISCAE\"   #> [67] \"DISTRTFL\" \"AEWITHFL\" \"ALIVDT\"   \"COHORT\"   \"TTYPE\"    \"STDSSDY\"  extraRowDataNames(object) #> [1] \"GeneID\"          \"SYMBOL\"          \"chromosome_name\""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"filters AnyHermesData object using default QC flags required annotations.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"","code":"filter(object, ...)  # S4 method for class 'AnyHermesData' filter(object, what = c(\"genes\", \"samples\"), annotation_required = \"size\")  # S4 method for class 'data.frame' filter(object, ...)  # S4 method for class 'ts' filter(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"object (AnyHermesData) object filter. ... additional arguments. (character) specify whether apply filter genes / samples. annotation_required (character) names required annotation columns genes. used genes filtered.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"filtered AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"genes without low expression (low_expression_flag) samples without low depth (low_depth_flag) technical failure (tech_failure_flag) remain returned filtered object. Also required gene annotation columns can specified, genes complete columns filtered . default size column, needed default normalization object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"internal implementation use subset() method since requires non-standard evaluation arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Filter AnyHermesData on Subset Passing Default QC Flags — filter","text":"","code":"a <- hermes_data dim(a) #> [1] 5085   20  # Filter genes and samples on default QC flags. result <- filter(a) dim(result) #> [1] 2064   18  # Filter only genes without low expression. result <- filter(a, what = \"genes\")  # Filter only samples with low depth and technical failure. result <- filter(a, what = \"samples\")  # Filter only genes, and require certain annotations to be present. result <- filter(a, what = \"genes\", annotation_required = c(\"size\"))"},{"path":"https://insightsengineering.github.io/hermes/reference/gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"GeneSpec Constructor — gene_spec","title":"GeneSpec Constructor — gene_spec","text":"Creates new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GeneSpec Constructor — gene_spec","text":"","code":"gene_spec(genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))"},{"path":"https://insightsengineering.github.io/hermes/reference/gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GeneSpec Constructor — gene_spec","text":"genes (named character NULL) gene IDs, names used labels available. fun (function NULL) summary function. NULL used multiple genes summarized returned matrix extract method. fun_name (string) name summary function.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/gene_spec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GeneSpec Constructor — gene_spec","text":"new GeneSpec object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/gene_spec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"GeneSpec Constructor — gene_spec","text":"","code":"gene_spec(\"GeneID:11185\") #> <GeneSpec> #>   Public: #>     clone: function (deep = FALSE)  #>     extract: function (assay)  #>     extract_data_frame: function (assay)  #>     get_gene_labels: function (genes = self$get_genes())  #>     get_genes: function ()  #>     get_label: function (genes = self$get_genes())  #>     initialize: function (genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))  #>     returns_vector: function ()  #>   Private: #>     fun: NULL #>     fun_name: NULL #>     gene_labels: GeneID:11185 #>     genes: GeneID:11185 gene_spec(c(\"GeneID:11185\", \"GeneID:10677\", \"GeneID:101928428\"), fun = colMeans) #> <GeneSpec> #>   Public: #>     clone: function (deep = FALSE)  #>     extract: function (assay)  #>     extract_data_frame: function (assay)  #>     get_gene_labels: function (genes = self$get_genes())  #>     get_genes: function ()  #>     get_label: function (genes = self$get_genes())  #>     initialize: function (genes = NULL, fun = NULL, fun_name = deparse(substitute(fun)))  #>     returns_vector: function ()  #>   Private: #>     fun: function (x, na.rm = FALSE, dims = 1, ...)  #>     fun_name: colMeans #>     gene_labels: GeneID:11185 GeneID:10677 GeneID:101928428 #>     genes: GeneID:11185 GeneID:10677 GeneID:101928428"},{"path":"https://insightsengineering.github.io/hermes/reference/genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Gene IDs Accessor — genes","title":"Gene IDs Accessor — genes","text":"Access gene IDs, .e. row names, AnyHermesData object nicely named accessor method.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gene IDs Accessor — genes","text":"","code":"genes(object)  # S4 method for class 'AnyHermesData' genes(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gene IDs Accessor — genes","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gene IDs Accessor — genes","text":"character vector gene IDs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gene IDs Accessor — genes","text":"","code":"a <- hermes_data genes(a) #>    [1] \"GeneID:11185\"     \"GeneID:10677\"     \"GeneID:101928428\" #>    [4] \"GeneID:100422835\" \"GeneID:102466731\" \"GeneID:64881\"     #>    [7] \"GeneID:286205\"    \"GeneID:8365\"      \"GeneID:6804\"      #>   [10] \"GeneID:100423018\" \"GeneID:23526\"     \"GeneID:102724693\" #>   [13] \"GeneID:10755\"     \"GeneID:283150\"    \"GeneID:101929282\" #>   [16] \"GeneID:57630\"     \"GeneID:101930284\" \"GeneID:102724480\" #>   [19] \"GeneID:9724\"      \"GeneID:647166\"    \"GeneID:339010\"    #>   [22] \"GeneID:4595\"      \"GeneID:11019\"     \"GeneID:407020\"    #>   [25] \"GeneID:116154\"    \"GeneID:27336\"     \"GeneID:51455\"     #>   [28] \"GeneID:26225\"     \"GeneID:102723987\" \"GeneID:5828\"      #>   [31] \"GeneID:100533181\" \"GeneID:10940\"     \"GeneID:55290\"     #>   [34] \"GeneID:2790\"      \"GeneID:101928197\" \"GeneID:277\"       #>   [37] \"GeneID:26818\"     \"GeneID:574033\"    \"GeneID:101929014\" #>   [40] \"GeneID:7200\"      \"GeneID:7386\"      \"GeneID:100422893\" #>   [43] \"GeneID:11189\"     \"GeneID:100130331\" \"GeneID:102723828\" #>   [46] \"GeneID:54936\"     \"GeneID:1088\"      \"GeneID:283234\"    #>   [49] \"GeneID:100505495\" \"GeneID:345462\"    \"GeneID:101927039\" #>   [52] \"GeneID:79908\"     \"GeneID:100130673\" \"GeneID:6277\"      #>   [55] \"GeneID:100846993\" \"GeneID:284836\"    \"GeneID:151827\"    #>   [58] \"GeneID:100507616\" \"GeneID:112812\"    \"GeneID:51098\"     #>   [61] \"GeneID:84278\"     \"GeneID:256643\"    \"GeneID:101927809\" #>   [64] \"GeneID:3149\"      \"GeneID:101929908\" \"GeneID:80201\"     #>   [67] \"GeneID:1553\"      \"GeneID:10966\"     \"GeneID:101928449\" #>   [70] \"GeneID:80024\"     \"GeneID:101928694\" \"GeneID:80305\"     #>   [73] \"GeneID:101927496\" \"GeneID:101927407\" \"GeneID:100996349\" #>   [76] \"GeneID:283624\"    \"GeneID:1057\"      \"GeneID:100287205\" #>   [79] \"GeneID:10919\"     \"GeneID:5686\"      \"GeneID:100302242\" #>   [82] \"GeneID:3454\"      \"GeneID:102725213\" \"GeneID:101930449\" #>   [85] \"GeneID:101927483\" \"GeneID:114770\"    \"GeneID:101928266\" #>   [88] \"GeneID:101927348\" \"GeneID:222894\"    \"GeneID:100316904\" #>   [91] \"GeneID:55128\"     \"GeneID:100874195\" \"GeneID:8685\"      #>   [94] \"GeneID:101927044\" \"GeneID:102466738\" \"GeneID:8295\"      #>   [97] \"GeneID:85456\"     \"GeneID:102725169\" \"GeneID:101927105\" #>  [100] \"GeneID:643355\"    \"GeneID:56931\"     \"GeneID:8354\"      #>  [103] \"GeneID:9717\"      \"GeneID:85016\"     \"GeneID:26222\"     #>  [106] \"GeneID:102725324\" \"GeneID:102724216\" \"GeneID:27333\"     #>  [109] \"GeneID:26999\"     \"GeneID:11212\"     \"GeneID:9024\"      #>  [112] \"GeneID:4359\"      \"GeneID:101927249\" \"GeneID:2055\"      #>  [115] \"GeneID:8325\"      \"GeneID:253982\"    \"GeneID:81544\"     #>  [118] \"GeneID:390067\"    \"GeneID:4261\"      \"GeneID:7472\"      #>  [121] \"GeneID:27299\"     \"GeneID:9383\"      \"GeneID:113730\"    #>  [124] \"GeneID:25984\"     \"GeneID:134265\"    \"GeneID:4141\"      #>  [127] \"GeneID:56651\"     \"GeneID:345456\"    \"GeneID:932\"       #>  [130] \"GeneID:3690\"      \"GeneID:22848\"     \"GeneID:102723454\" #>  [133] \"GeneID:100616330\" \"GeneID:7171\"      \"GeneID:102723659\" #>  [136] \"GeneID:9473\"      \"GeneID:391123\"    \"GeneID:9811\"      #>  [139] \"GeneID:147525\"    \"GeneID:338817\"    \"GeneID:219874\"    #>  [142] \"GeneID:3653\"      \"GeneID:221120\"    \"GeneID:102723329\" #>  [145] \"GeneID:100616419\" \"GeneID:440311\"    \"GeneID:220136\"    #>  [148] \"GeneID:100528022\" \"GeneID:64426\"     \"GeneID:114044\"    #>  [151] \"GeneID:574502\"    \"GeneID:378925\"    \"GeneID:54932\"     #>  [154] \"GeneID:2176\"      \"GeneID:124997\"    \"GeneID:57486\"     #>  [157] \"GeneID:2064\"      \"GeneID:340542\"    \"GeneID:10150\"     #>  [160] \"GeneID:10634\"     \"GeneID:25898\"     \"GeneID:126014\"    #>  [163] \"GeneID:390561\"    \"GeneID:100616136\" \"GeneID:8811\"      #>  [166] \"GeneID:100144748\" \"GeneID:693135\"    \"GeneID:4250\"      #>  [169] \"GeneID:10903\"     \"GeneID:56649\"     \"GeneID:440561\"    #>  [172] \"GeneID:958\"       \"GeneID:101927271\" \"GeneID:79092\"     #>  [175] \"GeneID:646670\"    \"GeneID:653513\"    \"GeneID:677837\"    #>  [178] \"GeneID:55795\"     \"GeneID:93349\"     \"GeneID:440570\"    #>  [181] \"GeneID:494332\"    \"GeneID:286177\"    \"GeneID:11156\"     #>  [184] \"GeneID:57864\"     \"GeneID:285766\"    \"GeneID:55776\"     #>  [187] \"GeneID:10804\"     \"GeneID:168451\"    \"GeneID:101930416\" #>  [190] \"GeneID:9377\"      \"GeneID:344758\"    \"GeneID:102725183\" #>  [193] \"GeneID:101929401\" \"GeneID:574494\"    \"GeneID:344967\"    #>  [196] \"GeneID:84331\"     \"GeneID:440386\"    \"GeneID:54504\"     #>  [199] \"GeneID:25893\"     \"GeneID:7109\"      \"GeneID:203100\"    #>  [202] \"GeneID:100289678\" \"GeneID:102724405\" \"GeneID:117608\"    #>  [205] \"GeneID:101927457\" \"GeneID:27044\"     \"GeneID:64396\"     #>  [208] \"GeneID:119692\"    \"GeneID:282616\"    \"GeneID:26716\"     #>  [211] \"GeneID:64236\"     \"GeneID:344892\"    \"GeneID:100996485\" #>  [214] \"GeneID:645434\"    \"GeneID:344905\"    \"GeneID:102465140\" #>  [217] \"GeneID:57037\"     \"GeneID:10777\"     \"GeneID:26276\"     #>  [220] \"GeneID:9435\"      \"GeneID:204851\"    \"GeneID:102723952\" #>  [223] \"GeneID:102465839\" \"GeneID:5201\"      \"GeneID:92521\"     #>  [226] \"GeneID:258\"       \"GeneID:5893\"      \"GeneID:3558\"      #>  [229] \"GeneID:9880\"      \"GeneID:64215\"     \"GeneID:2894\"      #>  [232] \"GeneID:389125\"    \"GeneID:102724585\" \"GeneID:102725138\" #>  [235] \"GeneID:100507054\" \"GeneID:340990\"    \"GeneID:102724534\" #>  [238] \"GeneID:100073347\" \"GeneID:387103\"    \"GeneID:284424\"    #>  [241] \"GeneID:693164\"    \"GeneID:100288637\" \"GeneID:390\"       #>  [244] \"GeneID:102724735\" \"GeneID:101926971\" \"GeneID:100874158\" #>  [247] \"GeneID:56943\"     \"GeneID:100131089\" \"GeneID:100500847\" #>  [250] \"GeneID:56923\"     \"GeneID:132946\"    \"GeneID:57448\"     #>  [253] \"GeneID:146956\"    \"GeneID:64284\"     \"GeneID:100271722\" #>  [256] \"GeneID:27352\"     \"GeneID:65217\"     \"GeneID:3065\"      #>  [259] \"GeneID:102724670\" \"GeneID:124975\"    \"GeneID:1431\"      #>  [262] \"GeneID:2194\"      \"GeneID:8318\"      \"GeneID:6144\"      #>  [265] \"GeneID:55907\"     \"GeneID:102725172\" \"GeneID:23401\"     #>  [268] \"GeneID:102725406\" \"GeneID:53828\"     \"GeneID:6510\"      #>  [271] \"GeneID:4712\"      \"GeneID:1911\"      \"GeneID:85478\"     #>  [274] \"GeneID:102723898\" \"GeneID:399687\"    \"GeneID:574411\"    #>  [277] \"GeneID:5324\"      \"GeneID:10135\"     \"GeneID:4300\"      #>  [280] \"GeneID:10818\"     \"GeneID:129401\"    \"GeneID:92305\"     #>  [283] \"GeneID:29780\"     \"GeneID:22941\"     \"GeneID:85300\"     #>  [286] \"GeneID:23237\"     \"GeneID:101929591\" \"GeneID:94239\"     #>  [289] \"GeneID:3157\"      \"GeneID:57718\"     \"GeneID:81550\"     #>  [292] \"GeneID:51411\"     \"GeneID:170627\"    \"GeneID:170825\"    #>  [295] \"GeneID:101927888\" \"GeneID:101929849\" \"GeneID:101929651\" #>  [298] \"GeneID:171546\"    \"GeneID:126668\"    \"GeneID:6730\"      #>  [301] \"GeneID:101929950\" \"GeneID:728492\"    \"GeneID:160\"       #>  [304] \"GeneID:101928156\" \"GeneID:1207\"      \"GeneID:140732\"    #>  [307] \"GeneID:2114\"      \"GeneID:101929425\" \"GeneID:4775\"      #>  [310] \"GeneID:8332\"      \"GeneID:55731\"     \"GeneID:7764\"      #>  [313] \"GeneID:85509\"     \"GeneID:101929756\" \"GeneID:2550\"      #>  [316] \"GeneID:151176\"    \"GeneID:145820\"    \"GeneID:100287616\" #>  [319] \"GeneID:84060\"     \"GeneID:1776\"      \"GeneID:8635\"      #>  [322] \"GeneID:102724839\" \"GeneID:283871\"    \"GeneID:91662\"     #>  [325] \"GeneID:142827\"    \"GeneID:10865\"     \"GeneID:100302184\" #>  [328] \"GeneID:504191\"    \"GeneID:833\"       \"GeneID:100422979\" #>  [331] \"GeneID:101930106\" \"GeneID:56169\"     \"GeneID:101927332\" #>  [334] \"GeneID:54793\"     \"GeneID:9617\"      \"GeneID:84798\"     #>  [337] \"GeneID:387748\"    \"GeneID:55622\"     \"GeneID:26057\"     #>  [340] \"GeneID:57646\"     \"GeneID:100049587\" \"GeneID:338588\"    #>  [343] \"GeneID:2350\"      \"GeneID:114880\"    \"GeneID:6721\"      #>  [346] \"GeneID:91445\"     \"GeneID:4836\"      \"GeneID:102723565\" #>  [349] \"GeneID:64853\"     \"GeneID:552891\"    \"GeneID:9123\"      #>  [352] \"GeneID:102724591\" \"GeneID:7596\"      \"GeneID:26098\"     #>  [355] \"GeneID:10652\"     \"GeneID:1580\"      \"GeneID:57405\"     #>  [358] \"GeneID:100874137\" \"GeneID:2009\"      \"GeneID:4734\"      #>  [361] \"GeneID:103581031\" \"GeneID:101930440\" \"GeneID:100033804\" #>  [364] \"GeneID:100996574\" \"GeneID:102465464\" \"GeneID:101241892\" #>  [367] \"GeneID:51567\"     \"GeneID:101929675\" \"GeneID:9254\"      #>  [370] \"GeneID:84890\"     \"GeneID:51804\"     \"GeneID:55889\"     #>  [373] \"GeneID:55630\"     \"GeneID:4541\"      \"GeneID:101928654\" #>  [376] \"GeneID:83446\"     \"GeneID:340441\"    \"GeneID:29063\"     #>  [379] \"GeneID:100132356\" \"GeneID:1400\"      \"GeneID:51517\"     #>  [382] \"GeneID:196374\"    \"GeneID:57180\"     \"GeneID:58510\"     #>  [385] \"GeneID:348174\"    \"GeneID:101929493\" \"GeneID:57231\"     #>  [388] \"GeneID:100847048\" \"GeneID:403273\"    \"GeneID:1947\"      #>  [391] \"GeneID:5858\"      \"GeneID:644093\"    \"GeneID:896\"       #>  [394] \"GeneID:102465489\" \"GeneID:729025\"    \"GeneID:196385\"    #>  [397] \"GeneID:283045\"    \"GeneID:5832\"      \"GeneID:101927391\" #>  [400] \"GeneID:1787\"      \"GeneID:4850\"      \"GeneID:80153\"     #>  [403] \"GeneID:124044\"    \"GeneID:10094\"     \"GeneID:84070\"     #>  [406] \"GeneID:101929994\" \"GeneID:100505692\" \"GeneID:203447\"    #>  [409] \"GeneID:1193\"      \"GeneID:102724927\" \"GeneID:4899\"      #>  [412] \"GeneID:6038\"      \"GeneID:222546\"    \"GeneID:83895\"     #>  [415] \"GeneID:102724811\" \"GeneID:4736\"      \"GeneID:147945\"    #>  [418] \"GeneID:84206\"     \"GeneID:55698\"     \"GeneID:3801\"      #>  [421] \"GeneID:645974\"    \"GeneID:767591\"    \"GeneID:56156\"     #>  [424] \"GeneID:26973\"     \"GeneID:9288\"      \"GeneID:327657\"    #>  [427] \"GeneID:7545\"      \"GeneID:407030\"    \"GeneID:4000\"      #>  [430] \"GeneID:100302158\" \"GeneID:102724232\" \"GeneID:58472\"     #>  [433] \"GeneID:9486\"      \"GeneID:8658\"      \"GeneID:56882\"     #>  [436] \"GeneID:51233\"     \"GeneID:102723976\" \"GeneID:390667\"    #>  [439] \"GeneID:347736\"    \"GeneID:100500842\" \"GeneID:144125\"    #>  [442] \"GeneID:79473\"     \"GeneID:153443\"    \"GeneID:283483\"    #>  [445] \"GeneID:101928947\" \"GeneID:101929628\" \"GeneID:3007\"      #>  [448] \"GeneID:154215\"    \"GeneID:4051\"      \"GeneID:345643\"    #>  [451] \"GeneID:101927670\" \"GeneID:102725405\" \"GeneID:100033417\" #>  [454] \"GeneID:85364\"     \"GeneID:1603\"      \"GeneID:90799\"     #>  [457] \"GeneID:2796\"      \"GeneID:23753\"     \"GeneID:55188\"     #>  [460] \"GeneID:101927722\" \"GeneID:284403\"    \"GeneID:338662\"    #>  [463] \"GeneID:474152\"    \"GeneID:143570\"    \"GeneID:101927507\" #>  [466] \"GeneID:100529209\" \"GeneID:574\"       \"GeneID:54101\"     #>  [469] \"GeneID:574465\"    \"GeneID:101928268\" \"GeneID:388695\"    #>  [472] \"GeneID:574447\"    \"GeneID:80313\"     \"GeneID:1071\"      #>  [475] \"GeneID:4628\"      \"GeneID:1176\"      \"GeneID:389906\"    #>  [478] \"GeneID:100616356\" \"GeneID:390181\"    \"GeneID:387787\"    #>  [481] \"GeneID:4988\"      \"GeneID:64101\"     \"GeneID:7021\"      #>  [484] \"GeneID:100500857\" \"GeneID:5089\"      \"GeneID:6860\"      #>  [487] \"GeneID:56131\"     \"GeneID:6533\"      \"GeneID:101927207\" #>  [490] \"GeneID:6262\"      \"GeneID:129450\"    \"GeneID:84750\"     #>  [493] \"GeneID:8370\"      \"GeneID:3832\"      \"GeneID:100996822\" #>  [496] \"GeneID:5961\"      \"GeneID:389124\"    \"GeneID:100616498\" #>  [499] \"GeneID:4618\"      \"GeneID:114960\"    \"GeneID:66008\"     #>  [502] \"GeneID:102723988\" \"GeneID:136242\"    \"GeneID:8242\"      #>  [505] \"GeneID:339302\"    \"GeneID:6431\"      \"GeneID:100313895\" #>  [508] \"GeneID:100381270\" \"GeneID:407043\"    \"GeneID:102723712\" #>  [511] \"GeneID:102724139\" \"GeneID:402778\"    \"GeneID:1647\"      #>  [514] \"GeneID:63874\"     \"GeneID:10149\"     \"GeneID:9344\"      #>  [517] \"GeneID:441455\"    \"GeneID:4539\"      \"GeneID:56140\"     #>  [520] \"GeneID:2827\"      \"GeneID:1475\"      \"GeneID:392509\"    #>  [523] \"GeneID:8763\"      \"GeneID:102465458\" \"GeneID:56242\"     #>  [526] \"GeneID:2180\"      \"GeneID:6522\"      \"GeneID:7570\"      #>  [529] \"GeneID:90835\"     \"GeneID:80301\"     \"GeneID:102724294\" #>  [532] \"GeneID:102466757\" \"GeneID:613\"       \"GeneID:101928555\" #>  [535] \"GeneID:664613\"    \"GeneID:8969\"      \"GeneID:26538\"     #>  [538] \"GeneID:100379661\" \"GeneID:402682\"    \"GeneID:653145\"    #>  [541] \"GeneID:101928207\" \"GeneID:9245\"      \"GeneID:51154\"     #>  [544] \"GeneID:727677\"    \"GeneID:102723786\" \"GeneID:720\"       #>  [547] \"GeneID:6160\"      \"GeneID:3936\"      \"GeneID:101930523\" #>  [550] \"GeneID:100506302\" \"GeneID:4026\"      \"GeneID:641373\"    #>  [553] \"GeneID:101929865\" \"GeneID:4858\"      \"GeneID:1622\"      #>  [556] \"GeneID:150248\"    \"GeneID:100506393\" \"GeneID:197003\"    #>  [559] \"GeneID:3083\"      \"GeneID:64518\"     \"GeneID:6617\"      #>  [562] \"GeneID:100129534\" \"GeneID:344148\"    \"GeneID:10460\"     #>  [565] \"GeneID:100313838\" \"GeneID:130752\"    \"GeneID:102724607\" #>  [568] \"GeneID:8985\"      \"GeneID:84793\"     \"GeneID:9546\"      #>  [571] \"GeneID:8667\"      \"GeneID:7319\"      \"GeneID:101926901\" #>  [574] \"GeneID:387254\"    \"GeneID:129790\"    \"GeneID:50700\"     #>  [577] \"GeneID:4148\"      \"GeneID:5191\"      \"GeneID:401944\"    #>  [580] \"GeneID:101926983\" \"GeneID:102725071\" \"GeneID:101928872\" #>  [583] \"GeneID:101928729\" \"GeneID:337867\"    \"GeneID:2040\"      #>  [586] \"GeneID:151009\"    \"GeneID:6774\"      \"GeneID:101930516\" #>  [589] \"GeneID:27239\"     \"GeneID:9527\"      \"GeneID:102724299\" #>  [592] \"GeneID:6405\"      \"GeneID:10623\"     \"GeneID:100616165\" #>  [595] \"GeneID:84514\"     \"GeneID:146336\"    \"GeneID:11316\"     #>  [598] \"GeneID:4794\"      \"GeneID:5778\"      \"GeneID:25833\"     #>  [601] \"GeneID:8337\"      \"GeneID:9534\"      \"GeneID:4985\"      #>  [604] \"GeneID:64805\"     \"GeneID:116337\"    \"GeneID:83548\"     #>  [607] \"GeneID:25828\"     \"GeneID:84440\"     \"GeneID:10778\"     #>  [610] \"GeneID:387978\"    \"GeneID:773\"       \"GeneID:390059\"    #>  [613] \"GeneID:221481\"    \"GeneID:3337\"      \"GeneID:841\"       #>  [616] \"GeneID:653645\"    \"GeneID:102725283\" \"GeneID:6737\"      #>  [619] \"GeneID:102724312\" \"GeneID:117581\"    \"GeneID:321\"       #>  [622] \"GeneID:101929410\" \"GeneID:27201\"     \"GeneID:81890\"     #>  [625] \"GeneID:10612\"     \"GeneID:128859\"    \"GeneID:100505989\" #>  [628] \"GeneID:7515\"      \"GeneID:27334\"     \"GeneID:64092\"     #>  [631] \"GeneID:102723603\" \"GeneID:51297\"     \"GeneID:7047\"      #>  [634] \"GeneID:22987\"     \"GeneID:101928722\" \"GeneID:27146\"     #>  [637] \"GeneID:728283\"    \"GeneID:100302140\" \"GeneID:102724285\" #>  [640] \"GeneID:83889\"     \"GeneID:3972\"      \"GeneID:8458\"      #>  [643] \"GeneID:64427\"     \"GeneID:100500823\" \"GeneID:10446\"     #>  [646] \"GeneID:27327\"     \"GeneID:54470\"     \"GeneID:102725185\" #>  [649] \"GeneID:23500\"     \"GeneID:55215\"     \"GeneID:101927191\" #>  [652] \"GeneID:83650\"     \"GeneID:152641\"    \"GeneID:102723992\" #>  [655] \"GeneID:84435\"     \"GeneID:6647\"      \"GeneID:178\"       #>  [658] \"GeneID:7733\"      \"GeneID:101930353\" \"GeneID:8460\"      #>  [661] \"GeneID:255119\"    \"GeneID:100996713\" \"GeneID:4047\"      #>  [664] \"GeneID:102725485\" \"GeneID:65008\"     \"GeneID:113115\"    #>  [667] \"GeneID:728741\"    \"GeneID:100287364\" \"GeneID:28960\"     #>  [670] \"GeneID:255239\"    \"GeneID:729683\"    \"GeneID:25895\"     #>  [673] \"GeneID:102466200\" \"GeneID:27133\"     \"GeneID:100128731\" #>  [676] \"GeneID:100616487\" \"GeneID:11018\"     \"GeneID:2967\"      #>  [679] \"GeneID:10466\"     \"GeneID:5563\"      \"GeneID:100128993\" #>  [682] \"GeneID:387319\"    \"GeneID:54544\"     \"GeneID:23517\"     #>  [685] \"GeneID:102465445\" \"GeneID:101241902\" \"GeneID:167838\"    #>  [688] \"GeneID:414062\"    \"GeneID:100505887\" \"GeneID:339803\"    #>  [691] \"GeneID:54097\"     \"GeneID:8907\"      \"GeneID:8735\"      #>  [694] \"GeneID:101340250\" \"GeneID:101929467\" \"GeneID:101929350\" #>  [697] \"GeneID:23127\"     \"GeneID:101930124\" \"GeneID:8852\"      #>  [700] \"GeneID:100874002\" \"GeneID:646892\"    \"GeneID:100874087\" #>  [703] \"GeneID:87769\"     \"GeneID:100126307\" \"GeneID:26291\"     #>  [706] \"GeneID:9085\"      \"GeneID:220416\"    \"GeneID:120376\"    #>  [709] \"GeneID:10526\"     \"GeneID:90990\"     \"GeneID:81035\"     #>  [712] \"GeneID:100129550\" \"GeneID:100873985\" \"GeneID:28971\"     #>  [715] \"GeneID:400612\"    \"GeneID:606293\"    \"GeneID:256281\"    #>  [718] \"GeneID:64096\"     \"GeneID:9114\"      \"GeneID:8161\"      #>  [721] \"GeneID:102724697\" \"GeneID:100873969\" \"GeneID:100506974\" #>  [724] \"GeneID:101929357\" \"GeneID:375056\"    \"GeneID:100033424\" #>  [727] \"GeneID:2577\"      \"GeneID:441687\"    \"GeneID:101929918\" #>  [730] \"GeneID:4692\"      \"GeneID:3040\"      \"GeneID:55729\"     #>  [733] \"GeneID:151188\"    \"GeneID:653123\"    \"GeneID:102723954\" #>  [736] \"GeneID:7433\"      \"GeneID:51388\"     \"GeneID:80059\"     #>  [739] \"GeneID:139562\"    \"GeneID:392188\"    \"GeneID:100302135\" #>  [742] \"GeneID:439\"       \"GeneID:100101938\" \"GeneID:345193\"    #>  [745] \"GeneID:102725008\" \"GeneID:390084\"    \"GeneID:81532\"     #>  [748] \"GeneID:341416\"    \"GeneID:619555\"    \"GeneID:103752554\" #>  [751] \"GeneID:7484\"      \"GeneID:6910\"      \"GeneID:653361\"    #>  [754] \"GeneID:100507674\" \"GeneID:400940\"    \"GeneID:9369\"      #>  [757] \"GeneID:100507006\" \"GeneID:102466726\" \"GeneID:348793\"    #>  [760] \"GeneID:132\"       \"GeneID:84146\"     \"GeneID:100505909\" #>  [763] \"GeneID:100009676\" \"GeneID:102725332\" \"GeneID:102465449\" #>  [766] \"GeneID:51257\"     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\"GeneID:100507065\" \"GeneID:492311\"    \"GeneID:100616280\" #> [1549] \"GeneID:8807\"      \"GeneID:10293\"     \"GeneID:163747\"    #> [1552] \"GeneID:25888\"     \"GeneID:54741\"     \"GeneID:100500897\" #> [1555] \"GeneID:100033453\" \"GeneID:23211\"     \"GeneID:9637\"      #> [1558] \"GeneID:100506142\" \"GeneID:2011\"      \"GeneID:283897\"    #> [1561] \"GeneID:53842\"     \"GeneID:646719\"    \"GeneID:148709\"    #> [1564] \"GeneID:51241\"     \"GeneID:101928068\" \"GeneID:65003\"     #> [1567] \"GeneID:401508\"    \"GeneID:27097\"     \"GeneID:26080\"     #> [1570] \"GeneID:124842\"    \"GeneID:284440\"    \"GeneID:102465250\" #> [1573] \"GeneID:6818\"      \"GeneID:100874110\" \"GeneID:102725189\" #> [1576] \"GeneID:5553\"      \"GeneID:100874188\" \"GeneID:5000\"      #> [1579] \"GeneID:100873768\" \"GeneID:80315\"     \"GeneID:101927901\" #> [1582] \"GeneID:150165\"    \"GeneID:100616223\" \"GeneID:4107\"      #> [1585] \"GeneID:23516\"     \"GeneID:100130992\" \"GeneID:83696\"     #> [1588] \"GeneID:101928618\" \"GeneID:22823\"     \"GeneID:2914\"      #> [1591] \"GeneID:56906\"     \"GeneID:101929964\" \"GeneID:101927288\" #> [1594] \"GeneID:102724775\" \"GeneID:158160\"    \"GeneID:101930064\" #> [1597] \"GeneID:51495\"     \"GeneID:3131\"      \"GeneID:1259\"      #> [1600] \"GeneID:284865\"    \"GeneID:91687\"     \"GeneID:51594\"     #> [1603] \"GeneID:55297\"     \"GeneID:7155\"      \"GeneID:102724184\" #> [1606] \"GeneID:22909\"     \"GeneID:10212\"     \"GeneID:101927492\" #> [1609] \"GeneID:85007\"     \"GeneID:401253\"    \"GeneID:168002\"    #> [1612] \"GeneID:58506\"     \"GeneID:25897\"     \"GeneID:25789\"     #> [1615] \"GeneID:23411\"     \"GeneID:654483\"    \"GeneID:102724861\" #> [1618] \"GeneID:8910\"      \"GeneID:101928754\" \"GeneID:6549\"      #> [1621] \"GeneID:9940\"      \"GeneID:101101776\" \"GeneID:91351\"     #> [1624] \"GeneID:101930002\" \"GeneID:101928225\" \"GeneID:653583\"    #> [1627] \"GeneID:55017\"     \"GeneID:79876\"     \"GeneID:768219\"    #> [1630] \"GeneID:101928135\" \"GeneID:677840\"    \"GeneID:51491\"     #> [1633] \"GeneID:2050\"      \"GeneID:11023\"     \"GeneID:102725201\" #> [1636] \"GeneID:2307\"      \"GeneID:101927464\" \"GeneID:814\"       #> [1639] \"GeneID:254102\"    \"GeneID:994\"       \"GeneID:153527\"    #> [1642] \"GeneID:10216\"     \"GeneID:2918\"      \"GeneID:200765\"    #> [1645] \"GeneID:894\"       \"GeneID:26791\"     \"GeneID:54495\"     #> [1648] \"GeneID:101927884\" \"GeneID:55540\"     \"GeneID:101927459\" #> [1651] \"GeneID:65059\"     \"GeneID:163175\"    \"GeneID:84848\"     #> [1654] \"GeneID:102724248\" \"GeneID:3267\"      \"GeneID:10238\"     #> [1657] \"GeneID:102724767\" \"GeneID:102723501\" \"GeneID:23090\"     #> [1660] \"GeneID:101927385\" \"GeneID:100500844\" \"GeneID:26097\"     #> [1663] \"GeneID:285550\"    \"GeneID:23317\"     \"GeneID:11199\"     #> [1666] \"GeneID:116461\"    \"GeneID:407040\"    \"GeneID:102724072\" #> [1669] 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\"GeneID:6102\"      \"GeneID:102723315\" #> [1753] \"GeneID:100302111\" \"GeneID:26515\"     \"GeneID:5729\"      #> [1756] \"GeneID:2959\"      \"GeneID:645206\"    \"GeneID:257397\"    #> [1759] \"GeneID:5369\"      \"GeneID:652276\"    \"GeneID:101929445\" #> [1762] \"GeneID:574518\"    \"GeneID:6474\"      \"GeneID:220988\"    #> [1765] \"GeneID:55616\"     \"GeneID:222962\"    \"GeneID:548645\"    #> [1768] \"GeneID:90324\"     \"GeneID:116938\"    \"GeneID:23498\"     #> [1771] \"GeneID:57477\"     \"GeneID:10230\"     \"GeneID:284047\"    #> [1774] \"GeneID:158801\"    \"GeneID:23154\"     \"GeneID:9321\"      #> [1777] \"GeneID:79071\"     \"GeneID:102723965\" \"GeneID:55870\"     #> [1780] \"GeneID:100287898\" \"GeneID:100033460\" \"GeneID:401093\"    #> [1783] \"GeneID:11151\"     \"GeneID:123591\"    \"GeneID:100507034\" #> [1786] \"GeneID:101927995\" \"GeneID:5162\"      \"GeneID:100862728\" #> [1789] \"GeneID:10955\"     \"GeneID:79694\"     \"GeneID:5916\"      #> [1792] 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\"GeneID:29969\"     #> [1834] \"GeneID:101926888\" \"GeneID:55037\"     \"GeneID:89777\"     #> [1837] \"GeneID:100616492\" \"GeneID:100131551\" \"GeneID:10200\"     #> [1840] \"GeneID:84643\"     \"GeneID:164045\"    \"GeneID:79097\"     #> [1843] \"GeneID:8945\"      \"GeneID:731789\"    \"GeneID:102725247\" #> [1846] \"GeneID:9612\"      \"GeneID:101927792\" \"GeneID:10613\"     #> [1849] \"GeneID:56005\"     \"GeneID:55689\"     \"GeneID:441282\"    #> [1852] \"GeneID:144321\"    \"GeneID:100886964\" \"GeneID:2584\"      #> [1855] \"GeneID:84084\"     \"GeneID:51805\"     \"GeneID:79023\"     #> [1858] \"GeneID:2662\"      \"GeneID:100616190\" \"GeneID:406902\"    #> [1861] \"GeneID:84283\"     \"GeneID:56897\"     \"GeneID:100419868\" #> [1864] \"GeneID:101928122\" \"GeneID:283238\"    \"GeneID:102725434\" #> [1867] \"GeneID:101926955\" \"GeneID:9537\"      \"GeneID:117145\"    #> [1870] \"GeneID:101928323\" \"GeneID:88\"        \"GeneID:101929654\" #> [1873] \"GeneID:388387\"    \"GeneID:64747\"     \"GeneID:101927082\" #> [1876] \"GeneID:5141\"      \"GeneID:100034743\" \"GeneID:441932\"    #> [1879] \"GeneID:222389\"    \"GeneID:5860\"      \"GeneID:102465506\" #> [1882] \"GeneID:27248\"     \"GeneID:3284\"      \"GeneID:55713\"     #> [1885] \"GeneID:101929478\" \"GeneID:2017\"      \"GeneID:5648\"      #> [1888] \"GeneID:65061\"     \"GeneID:26019\"     \"GeneID:7037\"      #> [1891] \"GeneID:51725\"     \"GeneID:100874531\" \"GeneID:101928098\" #> [1894] \"GeneID:22853\"     \"GeneID:158055\"    \"GeneID:3651\"      #> [1897] \"GeneID:390066\"    \"GeneID:102723375\" \"GeneID:2267\"      #> [1900] \"GeneID:387129\"    \"GeneID:7994\"      \"GeneID:79869\"     #> [1903] \"GeneID:100169959\" \"GeneID:102723382\" \"GeneID:55753\"     #> [1906] \"GeneID:100616476\" \"GeneID:25825\"     \"GeneID:100996465\" #> [1909] \"GeneID:6100\"      \"GeneID:651\"       \"GeneID:221584\"    #> [1912] \"GeneID:101928144\" \"GeneID:100036566\" \"GeneID:56729\"     #> [1915] \"GeneID:407027\"    \"GeneID:3911\"      \"GeneID:8890\"      #> [1918] \"GeneID:54620\"     \"GeneID:101928136\" \"GeneID:100500876\" #> [1921] \"GeneID:102723862\" \"GeneID:101927378\" \"GeneID:266\"       #> [1924] \"GeneID:102725009\" \"GeneID:84647\"     \"GeneID:102724492\" #> [1927] \"GeneID:3008\"      \"GeneID:3682\"      \"GeneID:101928220\" #> [1930] \"GeneID:26083\"     \"GeneID:8310\"      \"GeneID:1427\"      #> [1933] \"GeneID:10950\"     \"GeneID:647264\"    \"GeneID:101929657\" #> [1936] \"GeneID:5566\"      \"GeneID:100874127\" \"GeneID:9231\"      #> [1939] \"GeneID:102723687\" \"GeneID:284618\"    \"GeneID:8345\"      #> [1942] \"GeneID:440051\"    \"GeneID:58505\"     \"GeneID:9266\"      #> [1945] \"GeneID:55500\"     \"GeneID:6888\"      \"GeneID:285740\"    #> [1948] \"GeneID:102724326\" \"GeneID:3630\"      \"GeneID:158747\"    #> [1951] \"GeneID:51447\"     \"GeneID:57608\"     \"GeneID:3304\"      #> [1954] \"GeneID:728339\"    \"GeneID:286319\"    \"GeneID:677784\"    #> [1957] \"GeneID:613126\"    \"GeneID:25865\"     \"GeneID:1783\"      #> [1960] \"GeneID:79025\"     \"GeneID:3442\"      \"GeneID:102725307\" #> [1963] \"GeneID:101928955\" \"GeneID:9162\"      \"GeneID:79609\"     #> [1966] \"GeneID:28\"        \"GeneID:729862\"    \"GeneID:3754\"      #> [1969] \"GeneID:100302143\" \"GeneID:100532742\" \"GeneID:154754\"    #> [1972] \"GeneID:100422912\" \"GeneID:50840\"     \"GeneID:25774\"     #> [1975] \"GeneID:442721\"    \"GeneID:5438\"      \"GeneID:55738\"     #> [1978] \"GeneID:9592\"      \"GeneID:10849\"     \"GeneID:374860\"    #> [1981] \"GeneID:100996588\" \"GeneID:101929229\" \"GeneID:375316\"    #> [1984] \"GeneID:342666\"    \"GeneID:100506241\" \"GeneID:4879\"      #> [1987] \"GeneID:5370\"      \"GeneID:100137049\" \"GeneID:55079\"     #> [1990] \"GeneID:123036\"    \"GeneID:100287171\" \"GeneID:79026\"     #> [1993] \"GeneID:6003\"      \"GeneID:101929019\" \"GeneID:1522\"      #> [1996] \"GeneID:130497\"    \"GeneID:102723671\" \"GeneID:5173\"      #> [1999] \"GeneID:4223\"      \"GeneID:102724949\" \"GeneID:6996\"      #> [2002] \"GeneID:645027\"    \"GeneID:79171\"     \"GeneID:84898\"     #> [2005] \"GeneID:100996669\" \"GeneID:7139\"      \"GeneID:10933\"     #> [2008] \"GeneID:102725095\" \"GeneID:285533\"    \"GeneID:8711\"      #> [2011] \"GeneID:26774\"     \"GeneID:27247\"     \"GeneID:10844\"     #> [2014] \"GeneID:8634\"      \"GeneID:100128573\" \"GeneID:1802\"      #> [2017] \"GeneID:140886\"    \"GeneID:120065\"    \"GeneID:101060216\" #> [2020] \"GeneID:84931\"     \"GeneID:25987\"     \"GeneID:333929\"    #> [2023] \"GeneID:101929552\" \"GeneID:83606\"     \"GeneID:212\"       #> [2026] \"GeneID:83756\"     \"GeneID:102465517\" \"GeneID:121536\"    #> [2029] \"GeneID:11258\"     \"GeneID:283981\"    \"GeneID:9969\"      #> [2032] \"GeneID:3360\"      \"GeneID:723805\"    \"GeneID:187\"       #> [2035] \"GeneID:55175\"     \"GeneID:645520\"    \"GeneID:150696\"    #> [2038] \"GeneID:29085\"     \"GeneID:100874372\" \"GeneID:3126\"      #> [2041] \"GeneID:643770\"    \"GeneID:284294\"    \"GeneID:100507855\" #> [2044] \"GeneID:102466250\" \"GeneID:101060181\" \"GeneID:80196\"     #> [2047] \"GeneID:101930479\" \"GeneID:129531\"    \"GeneID:101928257\" #> [2050] \"GeneID:100422996\" \"GeneID:101928870\" \"GeneID:100847022\" #> [2053] \"GeneID:6948\"      \"GeneID:101928811\" \"GeneID:219790\"    #> [2056] \"GeneID:57498\"     \"GeneID:102467214\" \"GeneID:388697\"    #> [2059] \"GeneID:54657\"     \"GeneID:102724766\" \"GeneID:3043\"      #> [2062] \"GeneID:100268168\" \"GeneID:10090\"     \"GeneID:23276\"     #> [2065] \"GeneID:102724798\" \"GeneID:9846\"      \"GeneID:493856\"    #> [2068] \"GeneID:100033799\" \"GeneID:8204\"      \"GeneID:102725481\" #> [2071] \"GeneID:79160\"     \"GeneID:407004\"    \"GeneID:5709\"      #> [2074] \"GeneID:85009\"     \"GeneID:24148\"     \"GeneID:101928809\" #> [2077] \"GeneID:100419743\" \"GeneID:65080\"     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\"GeneID:101929759\" \"GeneID:79812\"     \"GeneID:29775\"     #> [4132] \"GeneID:93643\"     \"GeneID:100874088\" \"GeneID:125113\"    #> [4135] \"GeneID:100302201\" \"GeneID:89944\"     \"GeneID:102724731\" #> [4138] \"GeneID:693165\"    \"GeneID:1040\"      \"GeneID:54903\"     #> [4141] \"GeneID:101928019\" \"GeneID:27010\"     \"GeneID:100132813\" #> [4144] \"GeneID:387266\"    \"GeneID:10313\"     \"GeneID:145942\"    #> [4147] \"GeneID:400823\"    \"GeneID:102725110\" \"GeneID:9076\"      #> [4150] \"GeneID:253573\"    \"GeneID:653505\"    \"GeneID:81034\"     #> [4153] \"GeneID:23191\"     \"GeneID:91120\"     \"GeneID:728763\"    #> [4156] \"GeneID:102724660\" \"GeneID:3846\"      \"GeneID:8287\"      #> [4159] \"GeneID:1495\"      \"GeneID:100313830\" \"GeneID:100169956\" #> [4162] \"GeneID:3081\"      \"GeneID:729506\"    \"GeneID:100126330\" #> [4165] \"GeneID:643802\"    \"GeneID:57699\"     \"GeneID:440993\"    #> [4168] \"GeneID:574460\"    \"GeneID:9630\"      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\"GeneID:4218\"      \"GeneID:90874\"     \"GeneID:84125\"     #> [4870] \"GeneID:643827\"    \"GeneID:59269\"     \"GeneID:102724843\" #> [4873] \"GeneID:101448202\" \"GeneID:56937\"     \"GeneID:100113402\" #> [4876] \"GeneID:120224\"    \"GeneID:101927063\" \"GeneID:693136\"    #> [4879] \"GeneID:102724339\" \"GeneID:1266\"      \"GeneID:653489\"    #> [4882] \"GeneID:101927366\" \"GeneID:51147\"     \"GeneID:54847\"     #> [4885] \"GeneID:642636\"    \"GeneID:128408\"    \"GeneID:100616256\" #> [4888] \"GeneID:10047\"     \"GeneID:5583\"      \"GeneID:219854\"    #> [4891] \"GeneID:8803\"      \"GeneID:139599\"    \"GeneID:51548\"     #> [4894] \"GeneID:102723476\" \"GeneID:100142659\" \"GeneID:10734\"     #> [4897] \"GeneID:54887\"     \"GeneID:57497\"     \"GeneID:112939\"    #> [4900] \"GeneID:8263\"      \"GeneID:136853\"    \"GeneID:9986\"      #> [4903] \"GeneID:5781\"      \"GeneID:116496\"    \"GeneID:304\"       #> [4906] \"GeneID:2935\"      \"GeneID:23438\"     \"GeneID:389741\"    #> [4909] \"GeneID:51118\"     \"GeneID:101927467\" \"GeneID:101928361\" #> [4912] \"GeneID:102723607\" \"GeneID:79022\"     \"GeneID:100507387\" #> [4915] \"GeneID:79781\"     \"GeneID:100313772\" \"GeneID:60625\"     #> [4918] \"GeneID:102723310\" \"GeneID:377841\"    \"GeneID:64772\"     #> [4921] \"GeneID:201283\"    \"GeneID:378951\"    \"GeneID:60495\"     #> [4924] \"GeneID:100288432\" \"GeneID:255809\"    \"GeneID:100616318\" #> [4927] \"GeneID:326342\"    \"GeneID:100500894\" \"GeneID:23647\"     #> [4930] \"GeneID:2353\"      \"GeneID:4728\"      \"GeneID:101929770\" #> [4933] \"GeneID:100874236\" \"GeneID:6624\"      \"GeneID:102724862\" #> [4936] \"GeneID:400410\"    \"GeneID:7111\"      \"GeneID:101927992\" #> [4939] \"GeneID:100422968\" \"GeneID:643923\"    \"GeneID:4897\"      #> [4942] \"GeneID:348761\"    \"GeneID:26749\"     \"GeneID:6585\"      #> [4945] \"GeneID:101930248\" \"GeneID:157983\"    \"GeneID:29844\"     #> [4948] \"GeneID:3976\"      \"GeneID:25920\"     \"GeneID:27079\"     #> [4951] \"GeneID:9658\"      \"GeneID:101927046\" \"GeneID:22980\"     #> [4954] \"GeneID:8939\"      \"GeneID:101929560\" \"GeneID:91289\"     #> [4957] \"GeneID:388730\"    \"GeneID:5451\"      \"GeneID:905\"       #> [4960] \"GeneID:9053\"      \"GeneID:25788\"     \"GeneID:101928349\" #> [4963] \"GeneID:91526\"     \"GeneID:83460\"     \"GeneID:26354\"     #> [4966] \"GeneID:693124\"    \"GeneID:101929352\" \"GeneID:5046\"      #> [4969] \"GeneID:101730217\" \"GeneID:102723306\" \"GeneID:100422957\" #> [4972] \"GeneID:728734\"    \"GeneID:91754\"     \"GeneID:83452\"     #> [4975] \"GeneID:26022\"     \"GeneID:1910\"      \"GeneID:8840\"      #> [4978] \"GeneID:101927614\" \"GeneID:440087\"    \"GeneID:4494\"      #> [4981] \"GeneID:100527950\" \"GeneID:101927873\" \"GeneID:388813\"    #> [4984] \"GeneID:3298\"      \"GeneID:100616211\" \"GeneID:3925\"      #> [4987] \"GeneID:114881\"    \"GeneID:9479\"      \"GeneID:100130733\" #> [4990] \"GeneID:58495\"     \"GeneID:100422971\" \"GeneID:8801\"      #> [4993] \"GeneID:101929951\" \"GeneID:101928474\" \"GeneID:285172\"    #> [4996] \"GeneID:54856\"     \"GeneID:26819\"     \"GeneID:101928992\" #> [4999] \"GeneID:79001\"     \"GeneID:79782\"     \"GeneID:100101115\" #> [5002] \"GeneID:100101116\" \"GeneID:100101117\" \"GeneID:100101118\" #> [5005] \"GeneID:100101120\" \"GeneID:100132596\" \"GeneID:100289087\" #> [5008] \"GeneID:100533178\" \"GeneID:100874056\" \"GeneID:101929148\" #> [5011] \"GeneID:102723934\" \"GeneID:114758\"    \"GeneID:114760\"    #> [5014] \"GeneID:114761\"    \"GeneID:140032\"    \"GeneID:159119\"    #> [5017] \"GeneID:159125\"    \"GeneID:159162\"    \"GeneID:159163\"    #> [5020] \"GeneID:1617\"      \"GeneID:203611\"    \"GeneID:22829\"     #> [5023] \"GeneID:246119\"    \"GeneID:246122\"    \"GeneID:246126\"    #> [5026] \"GeneID:252946\"    \"GeneID:252949\"    \"GeneID:252950\"    #> [5029] \"GeneID:252951\"    \"GeneID:252952\"    \"GeneID:252953\"    #> [5032] \"GeneID:252954\"    \"GeneID:252955\"    \"GeneID:253175\"    #> [5035] \"GeneID:286554\"    \"GeneID:286557\"    \"GeneID:340618\"    #> [5038] \"GeneID:353513\"    \"GeneID:353515\"    \"GeneID:378948\"    #> [5041] \"GeneID:378949\"    \"GeneID:401629\"    \"GeneID:401630\"    #> [5044] \"GeneID:425057\"    \"GeneID:441543\"    \"GeneID:442867\"    #> [5047] \"GeneID:442868\"    \"GeneID:474148\"    \"GeneID:474149\"    #> [5050] \"GeneID:474150\"    \"GeneID:474151\"    \"GeneID:50858\"     #> [5053] \"GeneID:5616\"      \"GeneID:57054\"     \"GeneID:57055\"     #> [5056] \"GeneID:57135\"     \"GeneID:5940\"      \"GeneID:60439\"     #> [5059] \"GeneID:6192\"      \"GeneID:64593\"     \"GeneID:6736\"      #> [5062] \"GeneID:7258\"      \"GeneID:728137\"    \"GeneID:728395\"    #> [5065] \"GeneID:728403\"    \"GeneID:7404\"      \"GeneID:7544\"      #> [5068] \"GeneID:8284\"      \"GeneID:83259\"     \"GeneID:83864\"     #> [5071] \"GeneID:83866\"     \"GeneID:83867\"     \"GeneID:83868\"     #> [5074] \"GeneID:83869\"     \"GeneID:84559\"     \"GeneID:84672\"     #> [5077] \"GeneID:84673\"     \"GeneID:8653\"      \"GeneID:86614\"     #> [5080] \"GeneID:90665\"     \"GeneID:9082\"      \"GeneID:9083\"      #> [5083] \"GeneID:9084\"      \"GeneID:9087\"      \"GeneID:9426\""},{"path":"https://insightsengineering.github.io/hermes/reference/h_all_duplicated.html","id":null,"dir":"Reference","previous_headings":"","what":"Finding All Duplicates in Vector — h_all_duplicated","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"difference duplicated() also first occurrence duplicate flagged TRUE.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_all_duplicated.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"","code":"h_all_duplicated(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_all_duplicated.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"x vector data frame array NULL.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_all_duplicated.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"Logical vector flagging occurrences duplicate values TRUE.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_all_duplicated.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finding All Duplicates in Vector — h_all_duplicated","text":"","code":"h_all_duplicated(c(\"a\", \"a\", \"b\")) #> [1]  TRUE  TRUE FALSE duplicated(c(\"a\", \"a\", \"b\")) #> [1] FALSE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/hermes/reference/h_df_factors_with_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"helper function converts character logical variables factor variables data.frame. also sets explicit missing data level factor variables least one NA. Empty strings handled NA.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_df_factors_with_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"","code":"h_df_factors_with_explicit_na(data, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/hermes/reference/h_df_factors_with_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"data (data.frame) input data least one column. na_level (string) explicit missing level used.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_df_factors_with_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"modified data.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_df_factors_with_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion to Factors with Explicit Missing Level in a data.frame — h_df_factors_with_explicit_na","text":"","code":"dat <- data.frame(   a = c(NA, 2),   b = c(\"A\", NA),   c = c(\"C\", \"D\"),   d = factor(c(NA, \"X\")),   e = factor(c(\"Y\", \"Z\")) ) h_df_factors_with_explicit_na(dat) #>    a         b c         d e #> 1 NA         A C <Missing> Y #> 2  2 <Missing> D         X Z"},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":null,"dir":"Reference","previous_headings":"","what":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"helper functions performs differential expression analysis DESeq2::DESeq() given AnyHermesData input design matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"","code":"h_diff_expr_deseq2(object, design, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"object (HermesData) input. design (matrix) design matrix. ... additional arguments internally passed DESeq2::DESeq() (fitType, sfType, minReplicatesForReplace, useT, minmu).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"data frame columns log2_fc (estimated log2 fold change), stat (Wald statistic), p_val (raw p-value), adj_p_pval (Benjamini-Hochberg adjusted p-value).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"DESeq2_packagehermes","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_deseq2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DESeq2 Differential Expression Analysis — h_diff_expr_deseq2","text":"","code":"object <- hermes_data  # Create the design matrix corresponding to the factor of interest. design <- model.matrix(~SEX, colData(object))  # Then perform the `DESeq2` differential expression analysis. result <- h_diff_expr_deseq2(object, design) head(result) #>                 log2_fc      stat        p_val    adj_p_val #> GeneID:9834    5.859486  5.440035 5.327024e-08 0.0001852739 #> GeneID:221188  3.450713  4.805489 1.543734e-06 0.0026845539 #> GeneID:151242 -4.316426 -4.707534 2.507316e-06 0.0029068155 #> GeneID:9002    2.324969  4.390859 1.129039e-05 0.0097580091 #> GeneID:64344  -2.880611 -4.343419 1.402819e-05 0.0097580091 #> GeneID:4359    2.914210  4.206676 2.591542e-05 0.0113396717  # Change of the `fitType` can be required in some cases. result2 <- h_diff_expr_deseq2(object, design, fitType = \"local\") head(result2) #>                  log2_fc      stat        p_val    adj_p_val #> GeneID:9834    5.8595097  5.436419 5.436203e-08 0.0001605311 #> GeneID:221188  3.4507368  4.796226 1.616827e-06 0.0023872456 #> GeneID:151242 -4.3163441 -4.693049 2.691627e-06 0.0026494579 #> GeneID:9002    2.3249808  4.379230 1.190996e-05 0.0073970422 #> GeneID:64344  -2.8805945 -4.368250 1.252462e-05 0.0073970422 #> GeneID:51575  -0.7889652 -4.255997 2.081193e-05 0.0076822022"},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":null,"dir":"Reference","previous_headings":"","what":"limma/voom Differential Expression Analysis — h_diff_expr_voom","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"helper functions performs differential expression analysis voom method limma package (via limma::voom(), limma::lmFit() limma::eBayes()) given counts AnyHermesData object corresponding design matrix.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"","code":"h_diff_expr_voom(object, design, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"object (AnyHermesData) input. design (matrix) design matrix. ... additional arguments internally passed limma::eBayes() (robust, trend, proportion, winsor.tail.p, stdev.coef.lim).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"data frame columns log2_fc (estimated log2 fold change), stat (moderated t-statistic), p_val (raw p-value), adj_p_pval (Benjamini-Hochberg adjusted p-value).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"limma_packagehermes voom_methodhermes","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_diff_expr_voom.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"limma/voom Differential Expression Analysis — h_diff_expr_voom","text":"","code":"object <- hermes_data  # Create the design matrix corresponding to the factor of interest. design <- model.matrix(~SEX, colData(object))  # Then perform the differential expression analysis. result <- h_diff_expr_voom(object, design) head(result) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -4.239244 0.0004209192 0.9118348 #> GeneID:51227  -1.0467295 -4.032550 0.0006788432 0.9118348 #> GeneID:344558  1.6896266  3.824046 0.0010993677 0.9118348 #> GeneID:51575  -0.7760844 -3.746293 0.0013155805 0.9118348 #> GeneID:151242 -3.4358998 -3.570103 0.0019741997 0.9118348 #> GeneID:8904   -0.6100354 -3.542864 0.0021017199 0.9118348  # Sometimes we might want to specify method details. result2 <- h_diff_expr_voom(object, design, trend = TRUE, robust = TRUE) head(result2) #>                  log2_fc      stat        p_val adj_p_val #> GeneID:8000   -2.3200712 -3.848050 0.0008857274 0.8995289 #> GeneID:51227  -1.0467295 -3.724654 0.0011933484 0.8995289 #> GeneID:344558  1.6896266  3.684191 0.0013155791 0.8995289 #> GeneID:51575  -0.7760844 -3.498308 0.0020551283 0.8995289 #> GeneID:151242 -3.4358998 -3.441687 0.0023525055 0.8995289 #> GeneID:123036  2.9002547  3.431263 0.0024329189 0.8995289"},{"path":"https://insightsengineering.github.io/hermes/reference/h_ensembl_to_entrez_ids.html","id":null,"dir":"Reference","previous_headings":"","what":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"helper function queries BioMart translate Ensembl Entrez Gene IDs.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_ensembl_to_entrez_ids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"","code":"h_ensembl_to_entrez_ids(gene_ids, mart)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_ensembl_to_entrez_ids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"gene_ids (character)Ensembl gene IDs. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_ensembl_to_entrez_ids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"Character vector Entrez gene IDs.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_ensembl_to_entrez_ids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translation of Ensembl to Entrez Gene IDs — h_ensembl_to_entrez_ids","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_ensembl_to_entrez_ids(c(\"ENSG00000135407\", \"ENSG00000241644\"), mart) }"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_annotation_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotations from BioMart — h_get_annotation_biomart","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"Helper function query annotations biomaRt, cleaned gene IDs specific ID variable given biomaRt::Mart.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_annotation_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"","code":"h_get_annotation_biomart(gene_ids, id_var, mart)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_annotation_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"gene_ids (character) gene IDs, e.g. 10329, .e. already without Entrez GeneID prefix, ENSG00000241644 Ensembl gene ID. id_var (string) corresponding gene ID variable name BioMart, .e. entrezgene_id ensembl_gene_id. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_annotation_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"data frame columns: id_var (depending used) hgnc_symbol entrezgene_description chromosome_name size refseq_mrna refseq_peptide","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_annotation_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotations from BioMart — h_get_annotation_biomart","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_get_annotation_biomart(c(\"11185\", \"10677\"), id_var = \"entrezgene_id\", mart = mart) }"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_granges_by_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"function extracts chromosome number, start position end position transcripts given data.frame coordinates returned biomaRt::getBM() converts GRanges object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_granges_by_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"","code":"h_get_granges_by_id(coords, id)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_granges_by_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"coords (data.frame) returned biomaRt::getBM(), containing columns ensembl_gene_id, chromosome_name, exon_chrom_start, exon_chrom_end. id (string) single Ensembl gene ID convert coordinates .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_granges_by_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"GRange objects respective single gene ID.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_granges_by_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of BioMart Coordinates into GRanges — h_get_granges_by_id","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   attrs <- c(     \"ensembl_gene_id\",     \"ensembl_exon_id\",     \"chromosome_name\",     \"exon_chrom_start\",     \"exon_chrom_end\"   )   coords <- biomaRt::getBM(     filters = \"entrezgene_id\",     attributes = attrs,     values = c(\"11185\", \"10677\"),     mart = mart   )   h_get_granges_by_id(coords, \"ENSG00000135407\") }"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_size_biomart.html","id":null,"dir":"Reference","previous_headings":"","what":"Total Length of All Exons for Genes — h_get_size_biomart","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"helper function queries BioMart lengths genes adding exon lengths reducing overlaps.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_size_biomart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"","code":"h_get_size_biomart(gene_ids, id_var, mart)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_size_biomart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"gene_ids (character) gene IDs, e.g. 10329, .e. already without Entrez GeneID prefix, ENSG00000241644 Ensembl gene ID. id_var (string) corresponding gene ID variable name BioMart, .e. entrezgene_id ensembl_gene_id. mart (Mart) given biomaRt::Mart object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_size_biomart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"Named integer vector indicating gene lengths.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_get_size_biomart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total Length of All Exons for Genes — h_get_size_biomart","text":"","code":"if (interactive()) {   mart <- biomaRt::useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")   h_get_size_biomart(\"11185\", \"entrezgene_id\", mart)   h_get_size_biomart(\"ENSG00000215417\", \"ensembl_gene_id\", mart)   h_get_size_biomart(c(\"11185\", \"10677\"), \"entrezgene_id\", mart)   h_get_size_biomart(c(\"ENSG00000135407\", \"ENSG00000215417\"), \"ensembl_gene_id\", mart) }"},{"path":"https://insightsengineering.github.io/hermes/reference/h_has_req_annotations.html","id":null,"dir":"Reference","previous_headings":"","what":"Predicate for Required Annotations — h_has_req_annotations","title":"Predicate for Required Annotations — h_has_req_annotations","text":"helper function determines gene object whether required annotation columns filled.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_has_req_annotations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predicate for Required Annotations — h_has_req_annotations","text":"","code":"h_has_req_annotations(object, annotation_required)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_has_req_annotations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predicate for Required Annotations — h_has_req_annotations","text":"object (AnyHermesData) input object. annotation_required (character) names required annotation columns genes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_has_req_annotations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predicate for Required Annotations — h_has_req_annotations","text":"Named logical vector one value gene object, TRUE required annotation columns filled, otherwise FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/h_has_req_annotations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Predicate for Required Annotations — h_has_req_annotations","text":"","code":"object <- hermes_data result <- h_has_req_annotations(object, \"size\") all(result) #> [1] TRUE rowData(object)$size[1] <- NA # nolint which(!h_has_req_annotations(object, \"size\")) #> GeneID:11185  #>            1"},{"path":"https://insightsengineering.github.io/hermes/reference/h_map_pos.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Matching Map Values to Names — h_map_pos","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"used rename method. wraps assertions matching used several times.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_map_pos.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"","code":"h_map_pos(names, map)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_map_pos.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"names (character) original names. map (named character) mapping vector old (value) new (name) names. values must included names.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_map_pos.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"Integer vector positions map values names.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_map_pos.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Matching Map Values to Names — h_map_pos","text":"","code":"h_map_pos(c(\"a\", \"b\"), c(d = \"b\")) #> [1] 2"},{"path":"https://insightsengineering.github.io/hermes/reference/h_parens.html","id":null,"dir":"Reference","previous_headings":"","what":"Parenthesize a Character Vector — h_parens","title":"Parenthesize a Character Vector — h_parens","text":"helper function adds parentheses around element character vector.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_parens.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parenthesize a Character Vector — h_parens","text":"","code":"h_parens(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_parens.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parenthesize a Character Vector — h_parens","text":"x (character) inputs parenthesized.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_parens.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parenthesize a Character Vector — h_parens","text":"Character vector parentheses, except x blank string case returned unaltered.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_parens.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parenthesize a Character Vector — h_parens","text":"","code":"h_parens(\"bla\") #> [1] \"(bla)\" h_parens(\"\") #> [1] \"\" h_parens(c(\"bla\", \"bli\")) #> [1] \"(bla)\" \"(bli)\""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"function processes sample variables AnyHermesData corresponding principal components matrix, generates matrix R2 values.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"","code":"h_pca_df_r2_matrix(pca, df)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"pca (matrix) comprises principal components generated calc_pca(). df (data.frame) SummarizedExperiment::colData() AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"matrix R2 values combinations sample variables principal components.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"Note df columns numeric, character, factor logical included resulting matrix, variable types supported. addition, df columns constant, NA, character factor columns many levels also dropped analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_df_r2_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculation of R2 Matrix between Sample Variables and Principal Components — h_pca_df_r2_matrix","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Obtain the principal components. pca <- calc_pca(object)$x  # Obtain the `colData` as a `data.frame`. df <- as.data.frame(colData(object))  # Correlate them. r2_all <- h_pca_df_r2_matrix(pca, df) str(r2_all) #>  num [1:18, 1:39] 0.102 0.183 0.147 0.391 0.662 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:18] \"PC1\" \"PC2\" \"PC3\" \"PC4\" ... #>   ..$ : chr [1:39] \"AGEGRP\" \"AGE18\" \"STDDRS\" \"STDDRSD\" ...  # We can see that only about half of the columns from `df` were # used for the correlations. ncol(r2_all) #> [1] 39 ncol(df) #> [1] 74"},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"helper function calculates R2 values one sample variable AnyHermesData Principal Components (PCs) separately (one linear model fit PC).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"","code":"h_pca_var_rsquared(pca, x)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"pca (matrix) principal components matrix generated calc_pca(). x (vector) values one sample variable AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"vector R2 values principal component.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"Note case estimation problems PCs, NA returned .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_pca_var_rsquared.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculation of R2 between Sample Variable and Principal Components — h_pca_var_rsquared","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Obtain the principal components. pca <- calc_pca(object)$x  # Obtain the sample variable. x <- colData(object)$AGE18  # Correlate them. r2 <- h_pca_var_rsquared(pca, x)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_short_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a Short List of a Character Vector — h_short_list","title":"Make a Short List of a Character Vector — h_short_list","text":"helper function makes short list string, e.g. \", b, ..., z\" character vector, e.g. letters.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_short_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a Short List of a Character Vector — h_short_list","text":"","code":"h_short_list(x, sep = \", \", thresh = 3L)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_short_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a Short List of a Character Vector — h_short_list","text":"x (character) input listed. sep (string) separator use. thresh (count) threshold use, length x larger list shortened using ... ellipsis.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_short_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a Short List of a Character Vector — h_short_list","text":"String short list.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_short_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make a Short List of a Character Vector — h_short_list","text":"","code":"h_short_list(letters) #> [1] \"a, b, ..., z\" h_short_list(letters[1:3]) #> [1] \"a, b, c\" h_short_list(LETTERS[1:5], sep = \";\", thresh = 5L) #> [1] \"A;B;C;D;E\""},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":null,"dir":"Reference","previous_headings":"","what":"Stripping Prefix from Gene IDs — h_strip_prefix","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"helper function removes prefix possible delimiter vector gene IDs, digits returned.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"","code":"h_strip_prefix(gene_ids, prefix)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"gene_ids (character) original gene IDs including prefix optional delimiter digits. prefix (string) common prefix stripped away gene_ids.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"Character vector contains digits gene ID.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"currently used strip away GeneID prefix Entrez gene IDs can queried BioMart","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_strip_prefix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stripping Prefix from Gene IDs — h_strip_prefix","text":"","code":"h_strip_prefix(c(\"GeneID:11185\", \"GeneID:10677\"), prefix = \"GeneID\") #> [1] \"11185\" \"10677\""},{"path":"https://insightsengineering.github.io/hermes/reference/h_unique_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Creation of Unique Labels — h_unique_labels","title":"Creation of Unique Labels — h_unique_labels","text":"helper function generates set unique labels given unique IDs necessarily unique names.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_unique_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creation of Unique Labels — h_unique_labels","text":"","code":"h_unique_labels(ids, nms = NULL)"},{"path":"https://insightsengineering.github.io/hermes/reference/h_unique_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creation of Unique Labels — h_unique_labels","text":"ids (character NULL) unique IDs. nms (character NULL) necessarily unique names provided.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_unique_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creation of Unique Labels — h_unique_labels","text":"Character vector empty names replaced IDs non-unique names made unique appending IDs parentheses.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/h_unique_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creation of Unique Labels — h_unique_labels","text":"","code":"h_unique_labels(c(\"1\", \"2\", \"3\"), c(\"A\", \"B\", \"A\")) #> [1] \"A (1)\" \"B\"     \"A (3)\" h_unique_labels(NULL) #> NULL h_unique_labels(c(\"1\", \"2\", \"3\")) #> [1] \"1\" \"2\" \"3\""},{"path":"https://insightsengineering.github.io/hermes/reference/hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"hermes Package — hermes-package","title":"hermes Package — hermes-package","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"hermes Package — hermes-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@rconis.com Authors: Namrata Bhatia Stefanie Bienert Benoit Falquet Haocheng Li Jeff Luong Lyndsee Midori Zhang zhang.lyndsee@gene.com Alex Richardson Simona Rossomanno Tim Treis Mark Yan Naomi Chang Chendi Liao chendi.liao@roche.com Carolyn Zhang Joseph N. Paulson paulson.joseph@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/hermes_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Example HermesData Data — hermes_data","title":"Example HermesData Data — hermes_data","text":"example HermesData created underlying SummarizedExperiment::SummarizedExperiment object renaming descriptors align standard specification. already contains required columns rowData colData.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/hermes_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example HermesData Data — hermes_data","text":"","code":"hermes_data"},{"path":"https://insightsengineering.github.io/hermes/reference/hermes_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example HermesData Data — hermes_data","text":"HermesData object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/hermes_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example HermesData Data — hermes_data","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"useful function trying join genetic CDISC data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"","code":"inner_join_cdisc(   gene_data,   cdisc_data,   patient_key = \"USUBJID\",   additional_keys = character() )"},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"gene_data (data.frame DataFrame) genetic data. cdisc_data (data.frame) CDISC data (typically patient level data). patient_key (string) patient identifier. additional_keys (character) potential additional keys two data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"data.frame contains columns data sets merged keys.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"Columns contained data sets specified keys taken gene_data cdisc_data.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/inner_join_cdisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Inner Joining a Genes with a CDISC Data Set — inner_join_cdisc","text":"","code":"gene_data <- col_data_with_genes(hermes_data, \"counts\", gene_spec(\"GeneID:1820\")) cdisc_data <- data.frame(   USUBJID = head(gene_data$USUBJID, 10),   extra = 1:10 ) result <- inner_join_cdisc(gene_data, cdisc_data) #> Warning: Patients AB12345-CHN-7-id-28, AB12345-CHN-4-id-73, AB12345-RUS-1-id-52, AB12345-PAK-11-id-268, AB12345-CHN-13-id-102, AB12345-CHN-17-id-84, AB12345-BRA-11-id-9, AB12345-CHN-4-id-115, AB12345-CHN-15-id-245, AB12345-CHN-4-id-370 from gene data set were lost because they could not be joined to CDISC data set result #>                  USUBJID Filename       SampleID         AGEGRP AGE18 STDDRS #> 1   AB12345-CHN-1-id-307     eset 06520046C0018R 12 - <18 years  < 18  DEATH #> 2  AB12345-CHN-11-id-220     eset 06520105C0017R 12 - <18 years  < 18        #> 3  AB12345-CHN-15-id-201     eset 06520103C0017R    >= 18 years >= 18  DEATH #> 4  AB12345-CHN-15-id-262     eset 06520067C0018R   2 - <6 years  < 18        #> 5   AB12345-CHN-3-id-128     eset 06520011B0023R    >= 18 years >= 18  DEATH #> 6   AB12345-CHN-7-id-267     eset 06520092C0017R 12 - <18 years  < 18  DEATH #> 7  AB12345-NGA-11-id-173     eset 06520062C0017R  6 - <12 years  < 18  DEATH #> 8   AB12345-RUS-3-id-378     eset 06520063C0043R 12 - <18 years  < 18  DEATH #> 9   AB12345-USA-1-id-261     eset 06520022C0017R 12 - <18 years  < 18        #> 10   AB12345-USA-1-id-45     eset 06520001B0023R    >= 18 years >= 18  DEATH #>                                STDDRSD    STDSSDT              TRTDRS #> 1  DEATH DUE TO PROGRESSION OF DISEASE 07/24/2016 PROGRESSIVE DISEASE #> 2                                                 PROGRESSIVE DISEASE #> 3  DEATH DUE TO PROGRESSION OF DISEASE 08/12/2016 PROGRESSIVE DISEASE #> 4                                                 PROGRESSIVE DISEASE #> 5  DEATH DUE TO PROGRESSION OF DISEASE 05/31/2016       ADVERSE EVENT #> 6  DEATH DUE TO PROGRESSION OF DISEASE 02/16/2017 PROGRESSIVE DISEASE #> 7  DEATH DUE TO PROGRESSION OF DISEASE 09/11/2016 PROGRESSIVE DISEASE #> 8  DEATH DUE TO PROGRESSION OF DISEASE 08/05/2016 PROGRESSIVE DISEASE #> 9                                                 PROGRESSIVE DISEASE #> 10 DEATH DUE TO PROGRESSION OF DISEASE 01/08/2016 PROGRESSIVE DISEASE #>                   TRTDRSD BHDCIRC BHDCIRCU ADAFL BLANP BKPS BLKS BTANNER #> 1  PROGRESSION OF DISEASE      NA              Y    NA   80   80      NA #> 2  PROGRESSION OF DISEASE      NA              Y   100   NA  100      NA #> 3  PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #> 4  PROGRESSION OF DISEASE      NA              Y    NA  100  100      NA #> 5           ADVERSE EVENT      NA              Y   100   NA  100      NA #> 6  PROGRESSION OF DISEASE      NA              Y   100   NA  100      NA #> 7  PROGRESSION OF DISEASE      NA              Y    NA  100  100      NA #> 8  PROGRESSION OF DISEASE      NA              Y    90   NA   90      NA #> 9  PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #> 10 PROGRESSION OF DISEASE      NA              Y    NA   90   90      NA #>             FRPST     DURIDX    DURSAF    DURSUR LNTHRPY AENCIFL STUDYID #> 1  POST-MENARCHAL  61.667351 1.6755647  5.158111       5      NA AB12345 #> 2   PRE-MENARCHAL  14.981520 3.0882957  5.815195       4      NA AB12345 #> 3                  10.841889 0.9856263  3.055441       4      NA AB12345 #> 4                 131.088296 1.6755647 19.252567       3      NA AB12345 #> 5                  55.030801 0.9856263  5.026694       3      NA AB12345 #> 6                   7.687885 3.0225873 12.418891       1      NA AB12345 #> 7                  99.285421 3.5811088  6.340862       7      NA AB12345 #> 8                  93.568789 0.9856263  4.665298       3      NA AB12345 #> 9                  41.626283 1.6755647 18.858316       3      NA AB12345 #> 10                 45.733060 0.6570842  2.299795       2      NA AB12345 #>             RFSTDTC          RFENDTC         RFXSTDTC         RFXENDTC #> 1  2016-03-10T14:05 2016-03-31T15:49 2016-03-10T14:05 2016-03-31T15:49 #> 2  2017-04-11T12:35 2017-06-14T11:45 2017-04-11T12:35 2017-06-14T11:45 #> 3  2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10 2016-05-31T14:10 #> 4  2016-01-11T14:30 2016-02-01T13:30 2016-01-11T14:30 2016-02-01T13:30 #> 5  2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37 2016-01-14T12:37 #> 6  2016-02-12T11:05 2016-04-14T12:00 2016-02-12T11:05 2016-04-14T12:00 #> 7  2016-03-21T15:40 2016-06-08T18:00 2016-03-21T15:40 2016-06-08T18:00 #> 8  2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25 2016-03-24T14:25 #> 9  2016-02-08T12:37 2016-02-29T14:15 2016-02-08T12:37 2016-02-29T14:15 #> 10 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00 2015-11-05T11:00 #>       RFICDTC   RFPENDTC     DTHDTC DTHFL SITEID  INVID AGE  AGEU SEX #> 1  2016-02-18 2016-07-24 2016-07-24     Y 283495 223804  12 YEARS   F #> 2  2017-04-03                             283694 456732  15 YEARS   M #> 3  2016-05-11 2016-08-12 2016-08-12     Y 282087 468105  27 YEARS   F #> 4  2016-01-07                             282087 468105   2 YEARS   F #> 5  2015-12-30 2016-05-31 2016-05-31     Y 283495 223804  19 YEARS   F #> 6  2016-02-04 2017-02-16 2017-02-16     Y 280959  20842  16 YEARS   M #> 7  2016-03-02 2016-09-11 2016-09-11     Y 283497 241874   7 YEARS   F #> 8  2016-03-16 2016-08-05 2016-08-05     Y 284024 457432  13 YEARS   M #> 9  2016-02-01                             281049 457179  16 YEARS   F #> 10 2015-10-30 2016-01-08 2016-01-08     Y 283971 235545  19 YEARS   F #>                         RACE                 ETHNIC ARMCD       ARM ACTARMCD #> 1                      WHITE NOT HISPANIC OR LATINO  COH3  COHORT 3     COH3 #> 2                      WHITE NOT HISPANIC OR LATINO COH12 COHORT 12    COH12 #> 3                    UNKNOWN           NOT REPORTED COH9E COHORT 9E    COH9E #> 4                    UNKNOWN           NOT REPORTED  COH1  COHORT 1     COH1 #> 5                   MULTIPLE NOT HISPANIC OR LATINO  COH1  COHORT 1     COH1 #> 6                      WHITE NOT HISPANIC OR LATINO COH9O COHORT 9O    COH9O #> 7  BLACK OR AFRICAN AMERICAN     HISPANIC OR LATINO  COH6  COHORT 6     COH6 #> 8                      WHITE NOT HISPANIC OR LATINO  COH8  COHORT 8     COH8 #> 9                      ASIAN NOT HISPANIC OR LATINO  COH1  COHORT 1     COH1 #> 10                   UNKNOWN     HISPANIC OR LATINO  COH6  COHORT 6     COH6 #>       ACTARM COUNTRY      DMDTC DMDY BAGE BAGEU    BWT BWTU   BHT BHTU     BBMI #> 1   COHORT 3     CHN 2016-02-18  -21   12 YEARS  50.00   kg 157.0   cm 20.28480 #> 2  COHORT 12     CHN 2017-04-04   -7   15 YEARS  26.15   kg 136.0   cm 14.13819 #> 3   COHORT 9     CHN 2016-05-25   -6   27 YEARS  61.60   kg 173.0   cm 20.58204 #> 4   COHORT 1     CHN 2016-01-07   -4    2 YEARS  64.60   kg 177.1   cm 20.59659 #> 5   COHORT 1     CHN 2015-12-30  -15   19 YEARS  40.60   kg 154.0   cm 17.11924 #> 6   COHORT 9     CHN 2016-02-04   -8   16 YEARS  45.20   kg 161.1   cm 17.41596 #> 7   COHORT 6     NGA 2016-03-02  -19    7 YEARS  53.90   kg 176.0   cm 17.40057 #> 8   COHORT 8     RUS 2016-03-22   -2   13 YEARS  25.40   kg 125.0   cm 16.25600 #> 9   COHORT 1     USA 2016-02-01   -7   16 YEARS 104.70   kg 172.0   cm 35.39075 #> 10  COHORT 6     USA 2015-10-30   -6   19 YEARS  57.00   kg 172.0   cm 19.26717 #>    ITTFL SAFFL    INFCODT     RANDDT          TRTSDTC             TRTSDTM #> 1      Y     Y 2016-02-18 2016-03-09 2016-03-10T14:05 2016-03-10 14:05:00 #> 2      Y     Y 2017-04-03 2017-04-11 2017-04-11T12:35 2017-04-11 12:35:00 #> 3      Y     Y 2016-05-11 2016-05-31 2016-05-31T14:10 2016-05-31 14:10:00 #> 4      Y     Y 2016-01-07 2016-01-11 2016-01-11T14:30 2016-01-11 14:30:00 #> 5      Y     Y 2015-12-30 2016-01-14 2016-01-14T12:37 2016-01-14 12:37:00 #> 6      Y     Y 2016-02-04 2016-02-09 2016-02-12T11:05 2016-02-12 11:05:00 #> 7      Y     Y 2016-03-02 2016-03-21 2016-03-21T15:40 2016-03-21 15:40:00 #> 8      Y     Y 2016-03-16 2016-03-24 2016-03-24T14:25 2016-03-24 14:25:00 #> 9      Y     Y 2016-02-01 2016-02-03 2016-02-08T12:37 2016-02-08 12:37:00 #> 10     Y     Y 2015-10-30 2015-11-05 2015-11-05T11:00 2015-11-05 11:00:00 #>    TRTSTMF             TRTEDTM TRTETMF TRTDUR DISCSTUD DISCDEAT DISCAE DISTRTFL #> 1        S 2016-03-31 16:55:59       S     22        Y        Y      N        Y #> 2        S 2017-06-14 12:15:59       S     65        N        N      N        Y #> 3        S 2016-05-31 15:10:59       S      1        Y        Y      N        Y #> 4        S 2016-02-01 14:30:59       S     22        N        N      N        Y #> 5        S 2016-01-14 13:37:59       S      1        Y        Y      N        Y #> 6        S 2016-04-14 12:30:59       S     63        Y        Y      N        Y #> 7        S 2016-06-08 18:30:59       S     80        Y        Y      N        Y #> 8        S 2016-03-24 15:30:59       S      1        Y        Y      N        Y #> 9        S 2016-02-29 14:48:59       S     22        N        N      N        Y #> 10       S 2015-11-05 12:00:59       S      1        Y        Y      N        Y #>    AEWITHFL     ALIVDT #> 1         N 2016-07-24 #> 2         N 2017-09-27 #> 3         N 2016-08-12 #> 4         N 2017-08-15 #> 5         Y 2016-05-31 #> 6         N 2017-02-16 #> 7         N 2016-09-11 #> 8         N 2016-08-05 #> 9         N 2017-08-28 #> 10        N 2016-01-08 #>                                                           COHORT #> 1                                       Cohort 3 (NEUROBLASTOMA) #> 2                    Cohort 12 (ATYPICAL TERATOID RHABOID TUMOR) #> 3  Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION) #> 4                                       Cohort 1 (EWING SARCOMA) #> 5                                       Cohort 1 (EWING SARCOMA) #> 6  Cohort 9 (OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION) #> 7                                        Cohort 6 (OSTEOSARCOMA) #> 8                                         Cohort 8 (WILMS TUMOR) #> 9                                       Cohort 1 (EWING SARCOMA) #> 10                                       Cohort 6 (OSTEOSARCOMA) #>                                                                                                                                        TTYPE #> 1                                                                                                                              NEUROBLASTOMA #> 2                                                                                                           ATYPICAL TERATOID RHABDOID TUMOR #> 3                                                 GERM CELL TUMOR - YOLK SAC TUMOR (ENDODERMAL SINUS TUMOR) WITH DOCUMENTED PD-L1 EXPRESSION #> 4                                                                                                                              EWING SARCOMA #> 5                                                                                                                              EWING SARCOMA #> 6  OTHER TUMOR TYPES WITH DOCUMENTED PD-L1 EXPRESSION ON EITHER TUMOR CELLS OR IMMUNE CELLS (TUMORS TYPE MUST NOT BE INCLUDED IN LIST ABOVE) #> 7                                                                                                                               OSTEOSARCOMA #> 8                                                                                                                                WILMS TUMOR #> 9                                                                                                                              EWING SARCOMA #> 10                                                                                                                              OSTEOSARCOMA #>    STDSSDY low_depth_flag tech_failure_flag GeneID.1820 extra #> 1      137          FALSE             FALSE          16    10 #> 2       NA          FALSE             FALSE          54     4 #> 3       74          FALSE             FALSE         567     6 #> 4       NA          FALSE             FALSE         153     2 #> 5      139          FALSE             FALSE          49     1 #> 6      371          FALSE             FALSE         111     5 #> 7      175           TRUE             FALSE         180     9 #> 8      135           TRUE             FALSE          94     3 #> 9       NA          FALSE             FALSE         171     8 #> 10      65          FALSE             FALSE         118     7"},{"path":"https://insightsengineering.github.io/hermes/reference/isEmpty.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"method checks whether SummarizedExperiment::SummarizedExperiment object empty.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/isEmpty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"","code":"# S4 method for class 'SummarizedExperiment' isEmpty(x)"},{"path":"https://insightsengineering.github.io/hermes/reference/isEmpty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"x (SummarizedExperiment) object check.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/isEmpty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"Flag whether object empty.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/isEmpty.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty SummarizedExperiment — isEmpty,SummarizedExperiment-method","text":"","code":"isEmpty(summarized_experiment) #> [1] FALSE isEmpty(summarized_experiment[NULL, ]) #> [1] TRUE isEmpty(hermes_data) #> [1] FALSE"},{"path":"https://insightsengineering.github.io/hermes/reference/lapply.html","id":null,"dir":"Reference","previous_headings":"","what":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"Apply function experiments MAE.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/lapply.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"","code":"# S4 method for class 'MultiAssayExperiment' lapply(X, FUN, safe = TRUE, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/lapply.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"X (MultiAssayExperiment) input. FUN (function) applied experiment X. safe (flag) whether method skip experiments function fails. ... additional arguments passed FUN.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/lapply.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"MultiAssayExperiment object specified function applied.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/lapply.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"lapply method for MultiAssayExperiment — lapply,MultiAssayExperiment-method","text":"","code":"object <- multi_assay_experiment result <- lapply(object, normalize, safe = TRUE) #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. #> -- note: fitType='parametric', but the dispersion trend was not well captured by the #>    function: y = a/x + b, and a local regression fit was automatically substituted. #>    specify fitType='local' or 'mean' to avoid this message next time. # Similarly, all experiments in an MAE can be converted to HermesData class: result <- lapply(object, HermesData, safe = TRUE)"},{"path":"https://insightsengineering.github.io/hermes/reference/metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata Accessor and Setter — metadata","title":"Metadata Accessor and Setter — metadata","text":"methods access set metadata AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata Accessor and Setter — metadata","text":"x (AnyHermesData) object access metadata . value (list) list replace current metadata .","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata Accessor and Setter — metadata","text":"metadata list.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/metadata.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Metadata Accessor and Setter — metadata","text":"Note just inherits S4Vectors::metadata,Annotated-method().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata Accessor and Setter — metadata","text":"","code":"a <- hermes_data metadata(a) #> list() metadata(a) <- list(new = \"my metadata\") metadata(a) #> $new #> [1] \"my metadata\" #>"},{"path":"https://insightsengineering.github.io/hermes/reference/multi_assay_experiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Example MultiAssayExperiment Data — multi_assay_experiment","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"example MultiAssayExperiment::MultiAssayExperiment can used test data.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/multi_assay_experiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"","code":"multi_assay_experiment"},{"path":"https://insightsengineering.github.io/hermes/reference/multi_assay_experiment.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"MultiAssayExperiment::MultiAssayExperiment object 3 separate HermesData objects. first object contains 5 samples covers 1000 features (Entrez gene IDs). second object contains 9 samples 2500 features. third object contains 6 samples 1300 features.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/multi_assay_experiment.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example MultiAssayExperiment Data — multi_assay_experiment","text":"artificial dataset designed resemble real data.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"normalize() method normalizing input AnyHermesData according one specified normalization methods. results saved additional assays object. Possible normalization methods (implemented separate helper functions): cpm: Counts per Million (CPM). Separately sample, original counts genes divided library size sample, multiplied one million. appropriate normalization -sample comparisons. rpkm: Reads per Kilobase transcript per Million reads mapped (RPKM). gene count divided gene size (kilobases) divided library sizes sample (millions). allows within-sample comparisons, takes account gene sizes - longer genes always counts shorter genes. tpm: Transcripts per Million (TPM). addresses problem RPKM inconsistent across samples (can seen sum RPKM values vary sample sample). Therefore divide RPKM sum RPKM values sample, multiply one million. voom: VOOM normalization. essentially just slight variation CPM prior_count 0.5 combined lib_sizes increased 1 sample. Note required corresponding differential expression analysis, just provided complementary experimental normalization approach . vst: Variance stabilizing transformation. transform normalized count data genes approximately homoskedastic values (constant variance). rlog: transformation log2 scale values approximately homoskedastic values.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' normalize(   object,   methods = c(\"cpm\", \"rpkm\", \"tpm\", \"voom\", \"vst\"),   control = control_normalize(),   ... )  h_cpm(object, control = control_normalize())  h_rpkm(object, control = control_normalize())  h_tpm(object, control = control_normalize())  h_voom(object, control = control_normalize())  h_vst(object, control = control_normalize())  h_rlog(object, control = control_normalize())"},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"object (AnyHermesData) object normalize. methods (character) normalization methods use, see details. control (named list) settings produced control_normalize(). ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"AnyHermesData object additional assays containing normalized counts. control saved metadata object future reference.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"h_cpm(): calculates Counts per Million (CPM) normalized counts. h_rpkm(): calculates Reads per Kilobase per Million (RPKM) normalized counts. h_tpm(): calculates Transcripts per Million (TPM) normalized counts. h_voom(): calculates VOOM normalized counts. h_vst(): variance stabilizing transformation (vst) DESeq2 package. h_rlog(): regularized log transformation (rlog) DESeq2 package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Normalization of AnyHermesData Objects — normalize,AnyHermesData-method","text":"","code":"a <- hermes_data  # By default, log values are used with a prior count of 1 added to original counts. result <- normalize(a) assayNames(result) #> [1] \"counts\" \"cpm\"    \"rpkm\"   \"tpm\"    \"voom\"   \"vst\"    tpm <- assay(result, \"tpm\") tpm[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185          0.8626554       3.993877       3.591742 #> GeneID:10677          7.0670966       4.054655       3.289554 #> GeneID:101928428      0.0000000       0.000000       0.000000  # We can also work on original scale. result_orig <- normalize(a, control = control_normalize(log = FALSE)) tpm_orig <- assay(result_orig, \"tpm\") tpm_orig[1:3, 1:3] #>                  06520011B0023R 06520067C0018R 06520063C0043R #> GeneID:11185          0.8183821       14.93224       11.05653 #> GeneID:10677        133.0936048       15.61778        8.77810 #> GeneID:101928428      0.0000000        0.00000        0.00000  # Separate calculation of the CPM normalized counts. counts_cpm <- h_cpm(a) str(counts_cpm) #>  num [1:5085, 1:20] -0.453 8.252 -2.453 -2.453 -2.453 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the RPKM normalized counts. counts_rpkm <- h_rpkm(a) str(counts_rpkm) #>  num [1:5085, 1:20] -2.904 4.027 0.404 1.12 1.323 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the TPM normalized counts. counts_tpm <- h_tpm(a) str(counts_tpm) #>  num [1:5085, 1:20] 0.863 7.067 0 0 0 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the VOOM normalized counts. counts_voom <- h_voom(a) str(counts_voom) #>  num [1:5085, 1:20] -0.645 8.251 -3.453 -3.453 -3.453 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the vst transformation. counts_vst <- h_vst(a) str(counts_vst) #>  num [1:5085, 1:20] 3.03 10.6 1.78 1.78 1.78 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ...  # Separate calculation of the rlog transformation. counts_rlog <- h_rlog(a) str(counts_rlog) #>  num [1:5085, 1:20] 2.97 10.13 0 0 0 ... #>  - attr(*, \"dimnames\")=List of 2 #>   ..$ : chr [1:5085] \"GeneID:11185\" \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" ... #>   ..$ : chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ... #>  - attr(*, \"betaPriorVar\")= num 7.01 #>  - attr(*, \"intercept\")= num [1:5085, 1] 5.26 8.49 -Inf -Inf -Inf ..."},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"correlate() method analyses correlations (R2 values) sample variables AnyHermesData object principal components samples. corresponding autoplot() method can visualize results heatmap.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"","code":"# S4 method for class 'HermesDataPca' correlate(object, data)  # S4 method for class 'HermesDataPcaCor' autoplot(   object,   cor_colors = circlize::colorRamp2(c(-1, 0, 1), c(\"blue\", \"white\", \"red\")),   ... )"},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"object (HermesDataPca) input. can generated using calc_pca() function AnyHermesData. data (AnyHermesData) input used originally PCA. cor_colors (function) color scale function correlation values heatmap, produced circlize::colorRamp2(). ... arguments passed ComplexHeatmap::Heatmap().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"HermesDataPcaCor object R2 values sample variables.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"autoplot(HermesDataPcaCor): plot method uses ComplexHeatmap::Heatmap() function visualize HermesDataPcaCor object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/pca_cor_samplevar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation of Principal Components with Sample Variables — correlate,HermesDataPca-method","text":"","code":"object <- hermes_data %>%   add_quality_flags() %>%   filter() %>%   normalize()  # Perform PCA and then correlate the prinicipal components with the sample variables. object_pca <- calc_pca(object) result <- correlate(object_pca, object)  # Visualize the correlations in a heatmap. autoplot(result)   # We can also choose to not reorder the columns. autoplot(result, cluster_columns = FALSE)   # We can also choose break-points for color customization. autoplot(   result,   cor_colors = circlize::colorRamp2(     c(-0.5, -0.25, 0, 0.25, 0.5, 0.75, 1),     c(\"blue\", \"green\", \"purple\", \"yellow\", \"orange\", \"red\", \"brown\")   ) )"},{"path":"https://insightsengineering.github.io/hermes/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://insightsengineering.github.io/hermes/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result corresponding function call.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/pipe.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pipe operator — %>%","text":"","code":"hermes_data %>%   filter() %>%   normalize() %>%   summary() #> HermesData object with 18 samples of 2064 genes. #> - Library sizes across samples: mean 1997557, median 2007086, range 1595589 to 2374075 #> - Included assays (6): counts cpm ... voom vst #> - Additional gene information (3): GeneID SYMBOL chromosome_name #> - Additional sample information (72): Filename SampleID ... TTYPE #>   STDSSDY #> - Low expression genes (0): #> - Samples with too low depth or technical failures (0):"},{"path":"https://insightsengineering.github.io/hermes/reference/plot_all.html","id":null,"dir":"Reference","previous_headings":"","what":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"generates standard plots - histogram q-q plot library sizes, density plot (log) counts distributions, boxplot number number non-zero expressed genes per sample, stacked barplot low expression genes chromosome default setting.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/plot_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' autoplot(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/plot_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/plot_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"list ggplot objects draw_libsize_hist(), draw_libsize_qq(), draw_libsize_densities(), draw_nonzero_boxplot() draw_genes_barplot() functions default settings.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/plot_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All Standard Plots in Default Setting — autoplot,AnyHermesData-method","text":"","code":"result <- hermes_data autoplot(result)"},{"path":"https://insightsengineering.github.io/hermes/reference/prefix.html","id":null,"dir":"Reference","previous_headings":"","what":"Prefix Accessor — prefix","title":"Prefix Accessor — prefix","text":"Generic function access prefix object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/prefix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prefix Accessor — prefix","text":"","code":"prefix(object, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/prefix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prefix Accessor — prefix","text":"object (AnyHermesData) input. ... additional arguments.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/prefix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prefix Accessor — prefix","text":"prefix slot contents.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/prefix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prefix Accessor — prefix","text":"","code":"a <- hermes_data prefix(a) #> [1] \"GeneID\""},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Quality Flags — add_quality_flags","title":"Add Quality Flags — add_quality_flags","text":"function add_quality_flags() adds quality flag information AnyHermesData object: low_expression_flag: gene, counts many samples pass minimum expression Counts per Million (CPM) threshold. many, flags gene \"low expression\" gene. tech_failure_flag: first calculates Pearson correlation matrix sample wise CPM values, resulting matrix measuring correlation samples. compares average correlation per sample threshold - low, sample flagged \"technical failure\" sample. low_depth_flag: computes library size (total number counts) per sample. number low, sample flagged \"low depth\" sample. Separate helper functions internally used create flags, separate getter functions allow easy access quality control flags object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Quality Flags — add_quality_flags","text":"","code":"add_quality_flags(object, control = control_quality(), overwrite = FALSE)  h_low_expression_flag(object, control = control_quality())  h_low_depth_flag(object, control = control_quality())  h_tech_failure_flag(object, control = control_quality())  get_tech_failure(object)  get_low_depth(object)  get_low_expression(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Quality Flags — add_quality_flags","text":"object (AnyHermesData)  input. control (list)  list settings (thresholds etc.) used compute quality control flags, produced control_quality(). overwrite (flag) whether previously added flags may overwritten.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Quality Flags — add_quality_flags","text":"input object added quality flags.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Quality Flags — add_quality_flags","text":"object already variables mentioned part rowData colData (enforced validation method AnyHermesData), usually still NA initial object creation.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Add Quality Flags — add_quality_flags","text":"h_low_expression_flag(): creates low expression flag genes given control settings. h_low_depth_flag(): creates low depth (library size) flag samples given control settings. h_tech_failure_flag(): creates technical failure flag samples given control settings. get_tech_failure(): get technical failure flags samples. get_low_depth(): get low depth failure flags samples. get_low_expression(): get low expression failure flags genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/quality_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Quality Flags — add_quality_flags","text":"","code":"# Adding default quality flags to `AnyHermesData` object. object <- hermes_data result <- add_quality_flags(object) which(get_tech_failure(result) != get_tech_failure(object)) #> 06520046C0018R  #>             10  head(get_low_expression(result)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>            FALSE            FALSE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE  head(get_tech_failure(result)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_depth(result)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE   # It is possible to overwrite flags if needed, which will trigger a message. result2 <- add_quality_flags(result, control_quality(min_cpm = 1000), overwrite = TRUE) #> previously have added quality flags, but overwriting now  # Separate calculation of low expression flag. low_expr_flag <- h_low_expression_flag(   object,   control_quality(min_cpm = 500, min_cpm_prop = 0.9) ) length(low_expr_flag) == nrow(object) #> [1] TRUE head(low_expr_flag) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>             TRUE             TRUE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE   # Separate calculation of low depth flag. low_depth_flag <- h_low_depth_flag(object, control_quality(min_depth = 5)) length(low_depth_flag) == ncol(object) #> [1] TRUE head(low_depth_flag) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE   # Separate calculation of technical failure flag. tech_failure_flag <- h_tech_failure_flag(object, control_quality(min_corr = 0.35)) length(tech_failure_flag) == ncol(object) #> [1] TRUE head(tech_failure_flag) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_tech_failure(object)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE          FALSE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_depth(object)) #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>          FALSE          FALSE           TRUE          FALSE          FALSE  #> 06520103C0017R  #>          FALSE  head(get_low_expression(object)) #>     GeneID:11185     GeneID:10677 GeneID:101928428 GeneID:100422835  #>            FALSE             TRUE             TRUE             TRUE  #> GeneID:102466731     GeneID:64881  #>             TRUE             TRUE"},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":null,"dir":"Reference","previous_headings":"","what":"Query Gene Annotations from a Connection — query","title":"Query Gene Annotations from a Connection — query","text":"generic function query() interface querying gene annotations data base connection.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query Gene Annotations from a Connection — query","text":"","code":"query(genes, connection)  # S4 method for class 'character,ConnectionBiomart' query(genes, connection)"},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query Gene Annotations from a Connection — query","text":"genes (character) gene IDs. connection (connection class) data base connection object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query Gene Annotations from a Connection — query","text":"S4Vectors::DataFrame gene annotations. required : rownames identical input genes. colnames equal annotation columns .row_data_annotation_cols. Therefore, missing information needs properly included DataFrame NA entries.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Query Gene Annotations from a Connection — query","text":"method provided ConnectionBiomart class. However, framework extensible: simple add new connections corresponding query methods data bases, e.g. company internal data bases. Please make sure follow required format returned value. BioMart queries might return information genes. can due different versions used gene IDs queried Ensembl data base.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/query.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query Gene Annotations from a Connection — query","text":"","code":"if (interactive()) {   object <- hermes_data   connection <- connect_biomart(prefix(object))   result <- query(genes(object), connection)   head(result)   head(annotation(object)) }"},{"path":"https://insightsengineering.github.io/hermes/reference/rbind.html","id":null,"dir":"Reference","previous_headings":"","what":"Row Binding of AnyHermesData Objects — rbind","title":"Row Binding of AnyHermesData Objects — rbind","text":"method combines AnyHermesData objects samples different features interest (rows assays).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rbind.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row Binding of AnyHermesData Objects — rbind","text":"... (AnyHermesData) objects row bind.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rbind.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Row Binding of AnyHermesData Objects — rbind","text":"combined AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rbind.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Row Binding of AnyHermesData Objects — rbind","text":"Note just inherits SummarizedExperiment::rbind,SummarizedExperiment-method(). binding AnyHermesData object SummarizedExperiment::SummarizedExperiment object, result SummarizedExperiment::SummarizedExperiment object (general class). Note need unique gene IDs (row names) prefix across combined object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/rbind.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Row Binding of AnyHermesData Objects — rbind","text":"","code":"a <- hermes_data[1:2542, ] b <- hermes_data[2543:5085, ] result <- rbind(a, b) class(result) #> [1] \"HermesData\" #> attr(,\"package\") #> [1] \"hermes\""},{"path":"https://insightsengineering.github.io/hermes/reference/rename.html","id":null,"dir":"Reference","previous_headings":"","what":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"method renames columns rowData colData, well assays, SummarizedExperiment::SummarizedExperiment objects. increases flexibility since renaming can done conversion HermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"","code":"# S4 method for class 'SummarizedExperiment' rename(   x,   row_data = character(),   col_data = character(),   assays = character(),   ... )  # S4 method for class 'data.frame' rename(x, ...)"},{"path":"https://insightsengineering.github.io/hermes/reference/rename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"x (SummarizedExperiment) object rename contents . row_data (named character) mapping existing (right-hand side values) new (left-hand side names) column names rowData. col_data (named character) mapping existing (right-hand side values) new (left-hand side names) column names colData. assays (named character) mapping existing (right-hand side values) new (left-hand side names) assay names. ... additional arguments (used ).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"SummarizedExperiment::SummarizedExperiment object renamed contents.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/rename.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Renaming Contents of SummarizedExperiment Objects — rename,SummarizedExperiment-method","text":"","code":"x <- summarized_experiment # Use deliberately a non-standard assay name in this example. assayNames(x) <- \"count\"  # Rename `HGNC` to `symbol` in the `rowData`. x <- rename(x, row_data = c(symbol = \"HGNC\")) head(names(rowData(x))) #> [1] \"symbol\"       \"HGNCGeneName\" \"GeneID\"       \"Chromosome\"   \"StartBP\"      #> [6] \"EndBP\"         # Rename `LowDepthFlag` to `low_depth_flag` in `colData`. x <- rename(x, col_data = c(low_depth_flag = \"LowDepthFlag\")) tail(names(colData(x))) #> [1] \"ALIVDT\"               \"COHORT\"               \"TTYPE\"                #> [4] \"STDSSDY\"              \"low_depth_flag\"       \"TechnicalFailureFlag\"  # Rename assay `count` to `counts`. x <- rename(x, assays = c(counts = \"count\")) assayNames(x) #> [1] \"counts\""},{"path":"https://insightsengineering.github.io/hermes/reference/samples.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample IDs Accessor — samples,AnyHermesData-method","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"Access sample IDs, .e. col names, AnyHermesData object nicely named accessor method.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/samples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"","code":"# S4 method for class 'AnyHermesData' samples(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/samples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/samples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"character vector sample IDs.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/samples.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample IDs Accessor — samples,AnyHermesData-method","text":"","code":"a <- hermes_data samples(a) #>  [1] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" #>  [5] \"06520092C0017R\" \"06520103C0017R\" \"06520001B0023R\" \"06520022C0017R\" #>  [9] \"06520062C0017R\" \"06520046C0018R\" \"06520101B0017R\" \"06520047C0017R\" #> [13] \"06520024B0014R\" \"06520080B0023R\" \"06520093C0017R\" \"06520070C0018R\" #> [17] \"06520023C0018R\" \"06520099B0017R\" \"06520015C0016R\" \"06520019C0023R\""},{"path":"https://insightsengineering.github.io/hermes/reference/set_tech_failure.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Technical Failure Flags — set_tech_failure","title":"Set Technical Failure Flags — set_tech_failure","text":"Setter function allows user define sample manually technical failure.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/set_tech_failure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Technical Failure Flags — set_tech_failure","text":"","code":"set_tech_failure(object, sample_ids)"},{"path":"https://insightsengineering.github.io/hermes/reference/set_tech_failure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Technical Failure Flags — set_tech_failure","text":"object (AnyHermesData) input. sample_ids (character)  sample IDs flagged technical failures.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/set_tech_failure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Technical Failure Flags — set_tech_failure","text":"AnyHermesData object modified technical failure flags.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/set_tech_failure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Technical Failure Flags — set_tech_failure","text":"","code":"# Manually flag technical failures in a `AnyHermesData` object. object <- hermes_data get_tech_failure(object)[\"06520101B0017R\"] #> 06520101B0017R  #>          FALSE  result <- set_tech_failure(object, c(\"06520101B0017R\", \"06520047C0017R\")) get_tech_failure(result)[\"06520101B0017R\"] #> 06520101B0017R  #>           TRUE"},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":null,"dir":"Reference","previous_headings":"","what":"Show Method for AnyHermesData Objects — show,HermesData-method","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"show method displays high-level information AnyHermesData objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"","code":"# S4 method for class 'HermesData' show(object)  # S4 method for class 'RangedHermesData' show(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"object (AnyHermesData) input.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"None (invisible NULL), used side effect printing console.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"method used HermesData RangedHermesData objects. need define separately method used instead one inherited SummarizedExperiment::SummarizedExperiment.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/show.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show Method for AnyHermesData Objects — show,HermesData-method","text":"","code":"object <- hermes_data object #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY"},{"path":"https://insightsengineering.github.io/hermes/reference/subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Subsetting AnyHermesData Objects — subset","title":"Subsetting AnyHermesData Objects — subset","text":"method subsets AnyHermesData objects, based expressions involving rowData columns colData columns.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subsetting AnyHermesData Objects — subset","text":"x (AnyHermesData) object subset . subset (expression) logical expression based rowData columns select genes. select (expression) logical expression based colData columns select samples.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subsetting AnyHermesData Objects — subset","text":"subsetted AnyHermesData object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/subset.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subsetting AnyHermesData Objects — subset","text":"Note just inherits SummarizedExperiment::subset,SummarizedExperiment-method().","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/subset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subsetting AnyHermesData Objects — subset","text":"","code":"a <- hermes_data a #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset both genes and samples. subset(a, subset = low_expression_flag, select = DISCSTUD == \"N\") #> class: HermesData #> assays(1): counts #> genes(3021): GeneID:10677 GeneID:101928428 ... GeneID:9084 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(6): 06520067C0018R 06520105C0017R ... 06520023C0018R #>   06520099B0017R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset only genes. subset(a, subset = chromosome == \"2\") #> class: HermesData #> assays(1): counts #> genes(326): GeneID:101929282 GeneID:51455 ... GeneID:101927614 #>   GeneID:285172 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY  # Subset only samples. subset(a, select = AGE > 18) #> class: HermesData #> assays(1): counts #> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> additional gene information(3): GeneID SYMBOL chromosome_name #> samples(4): 06520011B0023R 06520103C0017R 06520001B0023R 06520080B0023R #> additional sample information(72): Filename SampleID ... TTYPE STDSSDY"},{"path":"https://insightsengineering.github.io/hermes/reference/summarized_experiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Example SummarizedExperiment Data — summarized_experiment","title":"Example SummarizedExperiment Data — summarized_experiment","text":"example SummarizedExperiment::SummarizedExperiment can used create HermesData object. already contains required columns rowData colData.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summarized_experiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example SummarizedExperiment Data — summarized_experiment","text":"","code":"summarized_experiment"},{"path":"https://insightsengineering.github.io/hermes/reference/summarized_experiment.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example SummarizedExperiment Data — summarized_experiment","text":"SummarizedExperiment::SummarizedExperiment object 20 samples covering 5085 features (Entrez gene IDs).","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summarized_experiment.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example SummarizedExperiment Data — summarized_experiment","text":"artificial dataset designed resemble real data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary Method for AnyHermesData Objects — summary","title":"Summary Method for AnyHermesData Objects — summary","text":"Provides concise summary content AnyHermesData objects.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary Method for AnyHermesData Objects — summary","text":"","code":"summary(object, ...)  # S4 method for class 'AnyHermesData' summary(object)  # S4 method for class 'HermesDataSummary' show(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary Method for AnyHermesData Objects — summary","text":"object (HermesDataSummary)  result summary method applied AnyHermesData object. ... used.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary Method for AnyHermesData Objects — summary","text":"object corresponding summary class, HermesDataSummary.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Summary Method for AnyHermesData Objects — summary","text":"summary(AnyHermesData): summary method AnyHermesData object creates HermesDataSummary object. show(HermesDataSummary): show method prints summary description HermesDataSummary object generated summary() method.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary Method for AnyHermesData Objects — summary","text":"","code":"object <- hermes_data object_summary <- summary(object)  # We can access parts of this S4 object with the `slot` function. str(object_summary) #> Formal class 'HermesDataSummary' [package \"hermes\"] with 10 slots #>   ..@ class_name            : chr \"HermesData\" #>   ..@ n_genes               : int 5085 #>   ..@ n_samples             : int 20 #>   ..@ additional_gene_info  : chr [1:3] \"GeneID\" \"SYMBOL\" \"chromosome_name\" #>   ..@ additional_sample_info: chr [1:72] \"Filename\" \"SampleID\" \"AGEGRP\" \"AGE18\" ... #>   ..@ no_qc_flags_filled    : logi FALSE #>   ..@ genes_fail            : chr [1:3021] \"GeneID:10677\" \"GeneID:101928428\" \"GeneID:100422835\" \"GeneID:102466731\" ... #>   ..@ samples_fail          : chr [1:2] \"06520063C0043R\" \"06520062C0017R\" #>   ..@ lib_sizes             : Named num [1:20] 5474927 5154958 4632496 5533212 5026848 ... #>   .. ..- attr(*, \"names\")= chr [1:20] \"06520011B0023R\" \"06520067C0018R\" \"06520063C0043R\" \"06520105C0017R\" ... #>   ..@ assay_names           : chr \"counts\" slotNames(object_summary) #>  [1] \"class_name\"             \"n_genes\"                \"n_samples\"              #>  [4] \"additional_gene_info\"   \"additional_sample_info\" \"no_qc_flags_filled\"     #>  [7] \"genes_fail\"             \"samples_fail\"           \"lib_sizes\"              #> [10] \"assay_names\"            slot(object_summary, \"lib_sizes\") #> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R  #>        5474927        5154958        4632496        5533212        5026848  #> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520046C0018R  #>        7262374        6408552        5286953        4778014        4990556  #> 06520101B0017R 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R  #>        4923925        5417510        5560720        4642530        5016838  #> 06520070C0018R 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R  #>        6464043        6080233        5314431        5426566        6139497   # Just calling the summary method like this will use the `show()` method. summary(object) #> HermesData object with 20 samples of 5085 genes. #> - Library sizes across samples: mean 5476759, median 5365970, range 4632496 to 7262374 #> - Included assays (1): counts #> - Additional gene information (3): GeneID SYMBOL chromosome_name #> - Additional sample information (72): Filename SampleID ... TTYPE #>   STDSSDY #> - Low expression genes (3021): GeneID:10677 GeneID:101928428 ... #>   GeneID:9084 GeneID:9426 #> - Samples with too low depth or technical failures (2): 06520063C0043R #>   06520062C0017R"},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivation of Top Genes — top_genes","title":"Derivation of Top Genes — top_genes","text":"top_genes() creates HermesDataTopGenes object, extends data.frame. contains two columns: expression: containing statistic values calculated summary_fun across columns. name: gene names. corresponding autoplot() method visualizes result barplot.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivation of Top Genes — top_genes","text":"","code":"top_genes(   object,   assay_name = \"counts\",   summary_fun = rowMeans,   n_top = if (is.null(min_threshold)) 10L else NULL,   min_threshold = NULL )  # S4 method for class 'HermesDataTopGenes' autoplot(   object,   x_lab = \"HGNC gene names\",   y_lab = paste0(object@summary_fun_name, \"(\", object@assay_name, \")\"),   title = \"Top most expressed genes\" )"},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivation of Top Genes — top_genes","text":"object (AnyHermedData) input. assay_name (string) name assay use sorting genes. summary_fun (function) summary statistics function apply across samples assay resulting numeric vector one value per gene. n_top (count NULL) selection criteria based number entries. min_threshold (number NULL ) selection criteria based minimum summary statistics threshold. x_lab (string) x-axis label. y_lab (string) y-axis label. title (string) plot title.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivation of Top Genes — top_genes","text":"HermesDataTopGenes object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Derivation of Top Genes — top_genes","text":"data frame sorted descending order expression top entries according selection criteria included. Note exactly one arguments n_top min_threshold must provided.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Derivation of Top Genes — top_genes","text":"autoplot(HermesDataTopGenes): Creates bar plot HermesDataTopGenes object, y axis shows expression statistics top genes x-axis.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/top_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Derivation of Top Genes — top_genes","text":"","code":"object <- hermes_data  # Default uses average of raw counts across samples to rank genes. top_genes(object) #>              expression         name #> GeneID:2335   390085.60  GeneID:2335 #> GeneID:79026  302684.20 GeneID:79026 #> GeneID:4627    60247.10  GeneID:4627 #> GeneID:667     59502.90   GeneID:667 #> GeneID:26986   58479.75 GeneID:26986 #> GeneID:6218    57782.15  GeneID:6218 #> GeneID:6205    50484.85  GeneID:6205 #> GeneID:811     42460.70   GeneID:811 #> GeneID:23215   41407.95 GeneID:23215 #> GeneID:4035    35884.20  GeneID:4035  # Instead of showing top 10 genes, can also set a minimum threshold on average counts. top_genes(object, n_top = NULL, min_threshold = 50000) #>              expression         name #> GeneID:2335   390085.60  GeneID:2335 #> GeneID:79026  302684.20 GeneID:79026 #> GeneID:4627    60247.10  GeneID:4627 #> GeneID:667     59502.90   GeneID:667 #> GeneID:26986   58479.75 GeneID:26986 #> GeneID:6218    57782.15  GeneID:6218 #> GeneID:6205    50484.85  GeneID:6205  # We can also use the maximum of raw counts across samples, by specifying a different # summary statistics function. result <- top_genes(object, summary_fun = rowMax)  # Finally we can produce barplots based on the results. autoplot(result, title = \"My top genes\")  autoplot(result, y_lab = \"Counts\", title = \"My top genes\")"},{"path":"https://insightsengineering.github.io/hermes/reference/validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"functions used internally therefore exported. work SummarizedExperiment::SummarizedExperiment objects, AnyHermesData objects defined successfully passing validation checks.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"","code":"validate_counts(object)  validate_cols(required, actual)  validate_row_data(object)  validate_col_data(object)  validate_names(object)  validate_prefix(object)"},{"path":"https://insightsengineering.github.io/hermes/reference/validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"object (SummarizedExperiment) object validate. required (character) required column names. actual (actual) actual column names.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"character vector validation failure messages, NULL case validation passes.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/validate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Internal Helper Functions for Validation of AnyHermesData Objects — validate","text":"validate_counts(): validates first assay counts containing non-missing, integer, non-negative values. validate_cols(): validates required column names contained actual column names. validate_row_data(): validates object contains rowData required columns. validate_col_data(): validates object contains colData required columns. validate_names(): validates object contains row column names. validate_prefix(): validates object prefix string contains alphabetic characters.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/wrap_in_mae.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap in MAE — wrap_in_mae","title":"Wrap in MAE — wrap_in_mae","text":"helper function wraps SummarizedExperiment objects MultiAssayExperiment (MAE) object.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/wrap_in_mae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap in MAE — wrap_in_mae","text":"","code":"wrap_in_mae(x, name = deparse(substitute(x)))"},{"path":"https://insightsengineering.github.io/hermes/reference/wrap_in_mae.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap in MAE — wrap_in_mae","text":"x (SummarizedExperiment) input create MAE object . name (string) experiment name use MAE x.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/wrap_in_mae.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap in MAE — wrap_in_mae","text":"MAE object experiment x given name.","code":""},{"path":"https://insightsengineering.github.io/hermes/reference/wrap_in_mae.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap in MAE — wrap_in_mae","text":"","code":"mae <- wrap_in_mae(summarized_experiment) mae[[\"summarized_experiment\"]] #> class: SummarizedExperiment  #> dim: 5085 20  #> metadata(0): #> assays(1): counts #> rownames(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426 #> rowData names(12): HGNC HGNCGeneName ... chromosome_name #>   LowExpressionFlag #> colnames(20): 06520011B0023R 06520067C0018R ... 06520015C0016R #>   06520019C0023R #> colData names(74): Filename SampleID ... LowDepthFlag #>   TechnicalFailureFlag"},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"miscellaneous-1-7-2-9003","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.7.2.9003","text":"Changed maintainer email address.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"enhancements-1-7-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.7.1","text":"New plotting function draw_heatmap produce heatmaps (normalized) counts.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"miscellaneous-1-7-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.7.1","text":"utility function df_cols_to_factor now also converts existing factors explicit missing levels. Version bump forcats dependency. Removed ggplot2 deprecation warning ..count...","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"enhancements-1-0-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.0.1","text":"Additional version argument connect_biomart specify Ensembl version.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"meta-1-0-0","dir":"Changelog","previous_headings":"","what":"Meta","title":"hermes 1.0.0","text":"First public release hermes package. Submission BioConductor.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"enhancements-1-0-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"hermes 1.0.0","text":"Better legends genes barplot correlation heatmap. Improved vignette layout using BioConductor style.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"miscellaneous-1-0-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 1.0.0","text":"New utility function cut_quantile cutting numeric vector quantiles. New utility function cat_with_newline concatenating printing newline. New check function check_proportion checks single proportion.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"new-features-0-1-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"hermes 0.1.1","text":"New function draw_scatterplot produce scatterplots two genes gene signatures. New function draw_boxplot boxplots gene expression values. New function draw_barplot barplots dichotomized gene expression counts two three percentile categories. New helper function wrap_in_mae wraps single SummarizedExperiment object MAE object. New method rename makes renaming columns rowData colData well assay names existing SummarizedExperiment objects much easier, step converting HermesData. New method lapply allows user apply function experiments MultiAssayExperiment. New method isEmpty checks whether SummarizedExperiment object empty. New gene filtering option n_top calc_pca function, allows filtering genes greatest variability across samples. New class GeneSpec specification genes gene signatures, see ?gene_spec simple construction. Inclusion gene signature functions colPrinComp1 colMeanZscores supplement standard column statistics functions. New helper function col_data_with_genes extracts sample variables saved colData together selected gene information combined data set. New helper function inner_join_cdisc joins genetic CDISC data sets.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"hermes 0.1.1","text":"normalize() now also works hermes package loaded, .e. can use hermes::normalize(). correlate() now also works factor variables sample variables HermesData object. add_quality_flags() longer return NA technical failure flags samples single gene contained input, instead vector FALSE ensure correct downstream functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"hermes 0.1.1","text":"Updated LICENCE README new package references. multi_assay_experiment now contains HermesData experiments, different patient IDs, one experiment normalized assays, multiple samples per patient one experiment. main HermesData example now saved package hermes_data, previous summarized_experiment still available. Note patient IDs changed new version align multi_assay_experiment. Renaming required rowData colData columns consistent standards use lowercase snake-case names. Annotation querying setting now flexible also allows query annotations required ones. Instead gene starts ends, total length gene exons now used annotation column size. Corresponding queries BioMart used return gene size. df_char_to_factor deprecated (can still used warning) replaced df_cols_to_factor, also converts logical variables factor variables. providing SummarizedExperiment objects containing DelayedMatrix assays HermesData() constructor, silently converted matrix assays ensure downstream functionality.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"hermes-010","dir":"Changelog","previous_headings":"","what":"hermes 0.1.0","title":"hermes 0.1.0","text":"First internal release hermes package, contains classes, methods functions import, quality-check, filter, normalize, analyze RNAseq counts data differential expression. hermes successor rnaseqTools R package. core functionality built BioConductor ecosystem, especially SummarizedExperiment class. New users first begin reading “Introduction hermes” vignette become familiar hermes concepts.","code":""},{"path":"https://insightsengineering.github.io/hermes/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"hermes 0.1.0","text":"Import RNAseq count data hermes ready format. Annotate gene information Ensembl database via biomaRt. Add quality control (QC) flags genes samples. Filter subset data set. Normalize counts. Produce descriptive plots. Perform principal components analysis. Produce templated QC Rmd report. Perform differential expression analysis.","code":""}]
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