diff --git a/main/404.html b/main/404.html
index a77f3fbc..eb3ba339 100644
--- a/main/404.html
+++ b/main/404.html
@@ -8,8 +8,8 @@
 <title>Page not found (404) • teal.modules.hermes</title>
 <script src="https://insightsengineering.github.io/teal.modules.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/teal.modules.hermes/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="https://insightsengineering.github.io/teal.modules.hermes/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://insightsengineering.github.io/teal.modules.hermes/deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="https://insightsengineering.github.io/teal.modules.hermes/deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="https://insightsengineering.github.io/teal.modules.hermes/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://insightsengineering.github.io/teal.modules.hermes/deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
+<link href="https://insightsengineering.github.io/teal.modules.hermes/deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
 <script src="https://insightsengineering.github.io/teal.modules.hermes/deps/headroom-0.11.0/headroom.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/search-1.0.0/fuse.min.js"></script><script src="https://insightsengineering.github.io/teal.modules.hermes/deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="https://insightsengineering.github.io/teal.modules.hermes/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 <link rel="stylesheet" href="https://insightsengineering.github.io/teal.modules.hermes/consent.css">
 <script src="https://insightsengineering.github.io/teal.modules.hermes/consent.js" type="text/javascript" charset="utf-8"></script>
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="https://insightsengineering.github.io/teal.modules.hermes/index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,16 +35,6 @@
 <li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/teal.modules.hermes/articles/index.html">Articles</a></li>
 <li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/teal.modules.hermes/news/index.html">Changelog</a></li>
       </ul>
-<!-- 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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
 <ul class="navbar-nav">
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/teal.modules.hermes"><span class="fa fa-github"></span></a></li>
       </ul>
diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html
index f148ff54..aa7e8390 100644
--- a/main/CODE_OF_CONDUCT.html
+++ b/main/CODE_OF_CONDUCT.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"><title>Contributor Covenant Code of Conduct • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/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="Contributor Covenant Code of Conduct"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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>Contributor Covenant Code of Conduct • teal.modules.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="Contributor Covenant Code of Conduct"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index cba961f3..f8f8e968 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.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"><title>Contribution Guidelines • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/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"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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 • teal.modules.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"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html
index 3011a322..8cda01cc 100644
--- a/main/LICENSE-text.html
+++ b/main/LICENSE-text.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"><title>License • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/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="License"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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>License • teal.modules.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="License"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/SECURITY.html b/main/SECURITY.html
index f598287e..d3bf1a8a 100644
--- a/main/SECURITY.html
+++ b/main/SECURITY.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"><title>Security Policy • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/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="Security Policy"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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>Security Policy • teal.modules.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="Security Policy"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/articles/Getting_Started.html b/main/articles/Getting_Started.html
index 59653df4..a7aee36a 100644
--- a/main/articles/Getting_Started.html
+++ b/main/articles/Getting_Started.html
@@ -8,8 +8,8 @@
 <title>Getting Started • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="../deps/font-awesome-6.4.2/css/v4-shims.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="Getting Started">
 <link rel="stylesheet" href="../consent.css">
 <script src="../consent.js" type="text/javascript" charset="utf-8"></script>
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,16 +35,6 @@
 <li class="active nav-item"><a class="nav-link" href="../articles/index.html">Articles</a></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul>
-<!-- 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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
 <ul class="navbar-nav">
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/teal.modules.hermes"><span class="fa fa-github"></span></a></li>
       </ul>
@@ -152,7 +142,7 @@ <h3 id="app-function">App function<a class="anchor" aria-label="anchor" href="#a
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">awesome_app</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">mae</span>, <span class="va">label</span> <span class="op">=</span> <span class="st">"My awesome app"</span><span class="op">)</span> <span class="op">{</span></span>
 <span>  <span class="va">mae_name</span> <span class="op">&lt;-</span> <span class="st">"MAE"</span></span>
-<span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">mae</span>, <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">)</span><span class="op">)</span></span>
+<span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">mae</span>, <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">)</span><span class="op">)</span></span>
 <span>  <span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span>
 <span>    data <span class="op">=</span> <span class="va">data</span>,</span>
 <span>    modules <span class="op">=</span> <span class="fu">teal</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/teal/latest-tag/reference/teal_modules.html" class="external-link">modules</a></span><span class="op">(</span></span>
@@ -174,7 +164,7 @@ <h3 id="testing-it">Testing it<a class="anchor" aria-label="anchor" href="#testi
 </h3>
 <p>To test this:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">awesome_app</span><span class="op">(</span><span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu">awesome_app</span><span class="op">(</span><span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></code></pre></div>
 </div>
 </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/main/articles/index.html b/main/articles/index.html
index 97cf034e..b4c377f5 100644
--- a/main/articles/index.html
+++ b/main/articles/index.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"><title>Articles • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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 • teal.modules.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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="active nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/authors.html b/main/authors.html
index 30b111a4..5f1f1ea4 100644
--- a/main/authors.html
+++ b/main/authors.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"><title>Authors and Citation • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/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"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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 • teal.modules.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"><link rel="stylesheet" href="consent.css"><script src="consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -123,14 +113,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024).
 <em>teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application</em>.
-R package version 0.1.6.9023,
+R package version 0.1.6.9024,
 https://github.com/insightsengineering/teal.modules.hermes/, <a href="https://insightsengineering.github.io/teal.modules.hermes/">https://insightsengineering.github.io/teal.modules.hermes/</a>.
 </p>
       <pre>@Manual{,
   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},
   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},
   year = {2024},
-  note = {R package version 0.1.6.9023,
+  note = {R package version 0.1.6.9024,
     https://github.com/insightsengineering/teal.modules.hermes/},
   url = {https://insightsengineering.github.io/teal.modules.hermes/},
 }</pre>
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index 8aa49e21..ca4dfd9c 100644
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deleted file mode 100644
index 6604a067..00000000
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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"); }
\ No newline at end of file
diff --git a/main/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf b/main/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
index 059a94e2..00000000
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diff --git a/main/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf b/main/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
deleted file mode 100644
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deleted file mode 100644
index 88b0367a..00000000
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diff --git a/main/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf b/main/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
deleted file mode 100644
index ba6cb258..00000000
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diff --git a/main/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2 b/main/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
deleted file mode 100644
index 23b1c47b..00000000
Binary files a/main/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2 and /dev/null differ
diff --git a/main/deps/font-awesome-6.4.2/css/all.css b/main/deps/font-awesome-6.5.2/css/all.css
similarity index 99%
rename from main/deps/font-awesome-6.4.2/css/all.css
rename to main/deps/font-awesome-6.5.2/css/all.css
index bdb6e3ae..151dd57c 100644
--- a/main/deps/font-awesome-6.4.2/css/all.css
+++ b/main/deps/font-awesome-6.5.2/css/all.css
@@ -1,7 +1,7 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * 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 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
 .fa {
   font-family: var(--fa-style-family, "Font Awesome 6 Free");
@@ -463,8 +463,8 @@
           transform: scale(-1, -1); }
 
 .fa-rotate-by {
-  -webkit-transform: rotate(var(--fa-rotate-angle, none));
-          transform: rotate(var(--fa-rotate-angle, none)); }
+  -webkit-transform: rotate(var(--fa-rotate-angle, 0));
+          transform: rotate(var(--fa-rotate-angle, 0)); }
 
 .fa-stack {
   display: inline-block;
@@ -2768,6 +2768,9 @@ readers do not read off random characters that represent icons */
 .fa-italic::before {
   content: "\f033"; }
 
+.fa-table-cells-column-lock::before {
+  content: "\e678"; }
+
 .fa-church::before {
   content: "\f51d"; }
 
@@ -4940,6 +4943,9 @@ readers do not read off random characters that represent icons */
 .fa-font::before {
   content: "\f031"; }
 
+.fa-table-cells-row-lock::before {
+  content: "\e67a"; }
+
 .fa-rupiah-sign::before {
   content: "\e23d"; }
 
@@ -5969,9 +5975,6 @@ readers do not read off random characters that represent icons */
 .fa-share::before {
   content: "\f064"; }
 
-.fa-arrow-turn-right::before {
-  content: "\f064"; }
-
 .fa-mail-forward::before {
   content: "\f064"; }
 
@@ -6421,6 +6424,9 @@ readers do not read off random characters that represent icons */
 .fa-ups:before {
   content: "\f7e0"; }
 
+.fa-pixiv:before {
+  content: "\e640"; }
+
 .fa-wpexplorer:before {
   content: "\f2de"; }
 
@@ -6481,6 +6487,9 @@ readers do not read off random characters that represent icons */
 .fa-drupal:before {
   content: "\f1a9"; }
 
+.fa-jxl:before {
+  content: "\e67b"; }
+
 .fa-hire-a-helper:before {
   content: "\f3b0"; }
 
@@ -6526,6 +6535,9 @@ readers do not read off random characters that represent icons */
 .fa-deskpro:before {
   content: "\f38f"; }
 
+.fa-brave:before {
+  content: "\e63c"; }
+
 .fa-sistrix:before {
   content: "\f3ee"; }
 
@@ -6694,6 +6706,9 @@ readers do not read off random characters that represent icons */
 .fa-cloudsmith:before {
   content: "\f384"; }
 
+.fa-opensuse:before {
+  content: "\e62b"; }
+
 .fa-pied-piper-alt:before {
   content: "\f1a8"; }
 
@@ -6778,6 +6793,9 @@ readers do not read off random characters that represent icons */
 .fa-kickstarter:before {
   content: "\f3bb"; }
 
+.fa-square-kickstarter:before {
+  content: "\f3bb"; }
+
 .fa-grav:before {
   content: "\f2d6"; }
 
@@ -6838,6 +6856,9 @@ readers do not read off random characters that represent icons */
 .fa-bluetooth-b:before {
   content: "\f294"; }
 
+.fa-square-letterboxd:before {
+  content: "\e62e"; }
+
 .fa-sticker-mule:before {
   content: "\f3f7"; }
 
@@ -6871,6 +6892,9 @@ readers do not read off random characters that represent icons */
 .fa-confluence:before {
   content: "\f78d"; }
 
+.fa-shoelace:before {
+  content: "\e60c"; }
+
 .fa-mdb:before {
   content: "\f8ca"; }
 
@@ -6994,6 +7018,9 @@ readers do not read off random characters that represent icons */
 .fa-envira:before {
   content: "\f299"; }
 
+.fa-google-scholar:before {
+  content: "\e63b"; }
+
 .fa-square-gitlab:before {
   content: "\e5ae"; }
 
@@ -7126,6 +7153,9 @@ readers do not read off random characters that represent icons */
 .fa-vine:before {
   content: "\f1ca"; }
 
+.fa-signal-messenger:before {
+  content: "\e663"; }
+
 .fa-paypal:before {
   content: "\f1ed"; }
 
@@ -7159,6 +7189,9 @@ readers do not read off random characters that represent icons */
 .fa-nfc-symbol:before {
   content: "\e531"; }
 
+.fa-mintbit:before {
+  content: "\e62f"; }
+
 .fa-ethereum:before {
   content: "\f42e"; }
 
@@ -7183,6 +7216,9 @@ readers do not read off random characters that represent icons */
 .fa-bimobject:before {
   content: "\f378"; }
 
+.fa-brave-reverse:before {
+  content: "\e63d"; }
+
 .fa-facebook-f:before {
   content: "\f39e"; }
 
@@ -7192,6 +7228,9 @@ readers do not read off random characters that represent icons */
 .fa-google-plus-square:before {
   content: "\f0d4"; }
 
+.fa-web-awesome:before {
+  content: "\e682"; }
+
 .fa-mandalorian:before {
   content: "\f50f"; }
 
@@ -7285,6 +7324,9 @@ readers do not read off random characters that represent icons */
 .fa-tencent-weibo:before {
   content: "\f1d5"; }
 
+.fa-letterboxd:before {
+  content: "\e62d"; }
+
 .fa-symfony:before {
   content: "\f83d"; }
 
@@ -7351,6 +7393,9 @@ readers do not read off random characters that represent icons */
 .fa-xbox:before {
   content: "\f412"; }
 
+.fa-square-web-awesome-stroke:before {
+  content: "\e684"; }
+
 .fa-searchengin:before {
   content: "\f3eb"; }
 
@@ -7423,6 +7468,9 @@ readers do not read off random characters that represent icons */
 .fa-cmplid:before {
   content: "\e360"; }
 
+.fa-upwork:before {
+  content: "\e641"; }
+
 .fa-facebook:before {
   content: "\f09a"; }
 
@@ -7456,6 +7504,9 @@ readers do not read off random characters that represent icons */
 .fa-whatsapp:before {
   content: "\f232"; }
 
+.fa-square-upwork:before {
+  content: "\e67c"; }
+
 .fa-slideshare:before {
   content: "\f1e7"; }
 
@@ -7534,6 +7585,9 @@ readers do not read off random characters that represent icons */
 .fa-sellsy:before {
   content: "\f213"; }
 
+.fa-square-web-awesome:before {
+  content: "\e683"; }
+
 .fa-sass:before {
   content: "\f41e"; }
 
@@ -7570,6 +7624,9 @@ readers do not read off random characters that represent icons */
 .fa-waze:before {
   content: "\f83f"; }
 
+.fa-bluesky:before {
+  content: "\e671"; }
+
 .fa-cc-jcb:before {
   content: "\f24b"; }
 
@@ -7597,6 +7654,9 @@ readers do not read off random characters that represent icons */
 .fa-supple:before {
   content: "\f3f9"; }
 
+.fa-webflow:before {
+  content: "\e65c"; }
+
 .fa-rebel:before {
   content: "\f1d0"; }
 
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.
+ */
+.fa{font-family:var(--fa-style-family,"Font Awesome 6 Free");font-weight:var(--fa-style,900)}.fa,.fa-brands,.fa-classic,.fa-regular,.fa-sharp,.fa-solid,.fab,.far,.fas{-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}.fa-classic,.fa-regular,.fa-solid,.far,.fas{font-family:"Font Awesome 6 Free"}.fa-brands,.fab{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:.625em;line-height:.1em;vertical-align:.225em}.fa-xs{font-size:.75em;line-height:.08333em;vertical-align:.125em}.fa-sm{font-size:.875em;line-height:.07143em;vertical-align:.05357em}.fa-lg{font-size:1.25em;line-height:.05em;vertical-align:-.075em}.fa-xl{font-size:1.5em;line-height:.04167em;vertical-align:-.125em}.fa-2xl{font-size:2em;line-height:.03125em;vertical-align:-.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-radius:var(--fa-border-radius,.1em);border:var(--fa-border-width,.08em) var(--fa-border-style,solid) var(--fa-border-color,#eee);padding:var(--fa-border-padding,.2em .25em .15em)}.fa-pull-left{float:left;margin-right:var(--fa-pull-margin,.3em)}.fa-pull-right{float:right;margin-left:var(--fa-pull-margin,.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(.28,.84,.42,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.28,.84,.42,1))}.fa-fade{-webkit-animation-name:fa-fade;animation-name:fa-fade;-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(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1))}.fa-beat-fade,.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)}.fa-beat-fade{-webkit-animation-name:fa-beat-fade;animation-name:fa-beat-fade;-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(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.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-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-shake,.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)}.fa-spin{-webkit-animation-name:fa-spin;animation-name:fa-spin;-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-beat-fade,.fa-bounce,.fa-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) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}}@keyframes fa-bounce{0%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}}@-webkit-keyframes fa-fade{50%{opacity:var(--fa-fade-opacity,.4)}}@keyframes fa-fade{50%{opacity:var(--fa-fade-opacity,.4)}}@-webkit-keyframes fa-beat-fade{0%,to{opacity:var(--fa-beat-fade-opacity,.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%,to{opacity:var(--fa-beat-fade-opacity,.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%,to{-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%,to{-webkit-transform:rotate(0deg);transform:rotate(0deg)}}@-webkit-keyframes fa-spin{0%{-webkit-transform:rotate(0deg);transform:rotate(0deg)}to{-webkit-transform:rotate(1turn);transform:rotate(1turn)}}@keyframes 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+
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diff --git a/main/deps/font-awesome-6.4.2/css/v4-shims.css b/main/deps/font-awesome-6.5.2/css/v4-shims.css
similarity index 99%
rename from main/deps/font-awesome-6.4.2/css/v4-shims.css
rename to main/deps/font-awesome-6.5.2/css/v4-shims.css
index a85953d1..ea60ea4d 100644
--- a/main/deps/font-awesome-6.4.2/css/v4-shims.css
+++ b/main/deps/font-awesome-6.5.2/css/v4-shims.css
@@ -1,7 +1,7 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * 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 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
 .fa.fa-glass:before {
   content: "\f000"; }
diff --git a/main/deps/font-awesome-6.4.2/css/v4-shims.min.css b/main/deps/font-awesome-6.5.2/css/v4-shims.min.css
similarity index 99%
rename from main/deps/font-awesome-6.4.2/css/v4-shims.min.css
rename to main/deps/font-awesome-6.5.2/css/v4-shims.min.css
index 64e4e8d8..09baf5fc 100644
--- a/main/deps/font-awesome-6.4.2/css/v4-shims.min.css
+++ b/main/deps/font-awesome-6.5.2/css/v4-shims.min.css
@@ -1,6 +1,6 @@
 /*!
- * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * 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 2023 Fonticons, Inc.
+ * Copyright 2024 Fonticons, Inc.
  */
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diff --git a/main/index.html b/main/index.html
index aba938d7..a38f6c09 100644
--- a/main/index.html
+++ b/main/index.html
@@ -8,8 +8,8 @@
 <title>RNA-Seq Analysis Modules to Add to a Teal Application • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet">
-<link href="deps/font-awesome-6.4.2/css/v4-shims.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="RNA-Seq Analysis Modules to Add to a Teal Application">
 <meta name="description" content="RNA-seq analysis teal modules based on the `hermes` package.">
 <meta property="og:description" content="RNA-seq analysis teal modules based on the `hermes` package.">
@@ -24,7 +24,7 @@
 
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,16 +37,6 @@
 <li class="nav-item"><a class="nav-link" href="articles/index.html">Articles</a></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul>
-<!-- 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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
 <ul class="navbar-nav">
 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/insightsengineering/teal.modules.hermes"><span class="fa fa-github"></span></a></li>
       </ul>
diff --git a/main/news/index.html b/main/news/index.html
index c098141f..6de90a18 100644
--- a/main/news/index.html
+++ b/main/news/index.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"><title>Changelog • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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 • teal.modules.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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -42,15 +32,15 @@ <h1>Changelog</h1>
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.1.6.9023" id="tealmoduleshermes-0169023">teal.modules.hermes 0.1.6.9023<a class="anchor" aria-label="anchor" href="#tealmoduleshermes-0169023"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.1.6.9024" id="tealmoduleshermes-0169024">teal.modules.hermes 0.1.6.9024<a class="anchor" aria-label="anchor" href="#tealmoduleshermes-0169024"></a></h2>
 <div class="section level4">
-<h4 id="miscellaneous-0-1-6-9023">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-1-6-9023"></a></h4>
+<h4 id="miscellaneous-0-1-6-9024">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-1-6-9024"></a></h4>
 <ul><li>Added placeholders for <code>assaySpec</code>, <code>adtteSpec</code> and <code>geneSpec</code> inputs when no option is selected.</li>
 <li>Disabled the select input for <code>assaySpec</code> and <code>adtteSpec</code> when there are no options available.</li>
 <li>For module developers: The module gets <code>teal_data</code> object in the UI and <code>reactive(&lt;teal_data&gt;)</code> in the server</li>
 </ul></div>
 <div class="section level4">
-<h4 id="enhancements-0-1-6-9023">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-1-6-9023"></a></h4>
+<h4 id="enhancements-0-1-6-9024">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-1-6-9024"></a></h4>
 <ul><li>Updated the documentation and vignettes with the new way of specifying data for <code><a href="https://insightsengineering.github.io/teal/latest-tag/reference/init.html" class="external-link">teal::init()</a></code>. The <code>data</code> argument accepts <code>teal_data</code> object.</li>
 <li>Added <code>teal.logger</code> functionality for logging changes in shiny inputs in all modules.</li>
 </ul></div>
diff --git a/main/pkgdown.yml b/main/pkgdown.yml
index 026a9109..712be17e 100644
--- a/main/pkgdown.yml
+++ b/main/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   Getting_Started: Getting_Started.html
-last_built: 2024-10-17T14:29Z
+last_built: 2024-12-12T14:43Z
 urls:
   reference: https://insightsengineering.github.io/teal.modules.hermes/reference
   article: https://insightsengineering.github.io/teal.modules.hermes/articles
diff --git a/main/reference/adtteSpecInput.html b/main/reference/adtteSpecInput.html
index aeef2524..6e51aca2 100644
--- a/main/reference/adtteSpecInput.html
+++ b/main/reference/adtteSpecInput.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"><title>Module Input for ADTTE Specification — adtteSpecInput • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Input for ADTTE Specification — adtteSpecInput"><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>Module Input for ADTTE Specification — adtteSpecInput • teal.modules.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="Module Input for ADTTE Specification — adtteSpecInput"><meta name="description" content="
 This defines the input for the ADTTE specification."><meta property="og:description" content="
 This defines the input for the ADTTE specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/adtteSpecServer.html b/main/reference/adtteSpecServer.html
index 35905db2..2949db94 100644
--- a/main/reference/adtteSpecServer.html
+++ b/main/reference/adtteSpecServer.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"><title>Module Server for ADTTE Specification — adtteSpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for ADTTE Specification — adtteSpecServer"><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>Module Server for ADTTE Specification — adtteSpecServer • teal.modules.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="Module Server for ADTTE Specification — adtteSpecServer"><meta name="description" content="
 This defines the server part for the ADTTE specification. The resulting data
 set binned_adtte_subset contains the subset of ADTTE selected by the time-to-event
 endpoint, joined together with the gene information extracted from specified assay
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,16 +29,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -231,7 +221,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="va">ADSL</span> <span class="op">&lt;-</span> <span class="fu">teal.data</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/teal.data/latest-tag/reference/rADSL.html" class="external-link">rADSL</a></span></span></span>
 <span class="r-in"><span>    <span class="va">ADTTE</span> <span class="op">&lt;-</span> <span class="fu">teal.modules.hermes</span><span class="fu">::</span><span class="va"><a href="rADTTE.html">rADTTE</a></span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>      <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>is_event <span class="op">=</span> <span class="va">.data</span><span class="op">$</span><span class="va">CNSR</span> <span class="op">==</span> <span class="fl">0</span><span class="op">)</span></span></span>
-<span class="r-in"><span>    <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
+<span class="r-in"><span>    <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
 <span class="r-in"><span>  <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">datanames</span> <span class="op">&lt;-</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">"ADSL"</span>, <span class="st">"ADTTE"</span>, <span class="st">"MAE"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="fu">datanames</span><span class="op">(</span><span class="va">data</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datanames</span></span></span>
diff --git a/main/reference/assaySpecInput.html b/main/reference/assaySpecInput.html
index 08b400e3..ec28e704 100644
--- a/main/reference/assaySpecInput.html
+++ b/main/reference/assaySpecInput.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"><title>Module Input for Assay Specification — assaySpecInput • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Input for Assay Specification — assaySpecInput"><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>Module Input for Assay Specification — assaySpecInput • teal.modules.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="Module Input for Assay Specification — assaySpecInput"><meta name="description" content="
 This defines the input for the assay specification."><meta property="og:description" content="
 This defines the input for the assay specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/assaySpecServer.html b/main/reference/assaySpecServer.html
index 31a08b24..fecc0fa9 100644
--- a/main/reference/assaySpecServer.html
+++ b/main/reference/assaySpecServer.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"><title>Module Server for Assay Specification — assaySpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for Assay Specification — assaySpecServer"><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>Module Server for Assay Specification — assaySpecServer • teal.modules.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="Module Server for Assay Specification — assaySpecServer"><meta name="description" content="
 This defines the server part for the assay specification."><meta property="og:description" content="
 This defines the server part for the assay specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -119,7 +109,7 @@ <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>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">my_app</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>    data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>    modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
diff --git a/main/reference/assert_adtte_vars.html b/main/reference/assert_adtte_vars.html
index 8b2dbdbb..54c11132 100644
--- a/main/reference/assert_adtte_vars.html
+++ b/main/reference/assert_adtte_vars.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"><title>Check for ADTTE Variables — assert_adtte_vars • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 ADTTE Variables — assert_adtte_vars"><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>Check for ADTTE Variables — assert_adtte_vars • teal.modules.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 ADTTE Variables — assert_adtte_vars"><meta name="description" content="
 Check whether x is a list of ADTTE variables."><meta property="og:description" content="
 Check whether x is a list of ADTTE variables."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/assert_summary_funs.html b/main/reference/assert_summary_funs.html
index 76d0d6ce..65b07ddd 100644
--- a/main/reference/assert_summary_funs.html
+++ b/main/reference/assert_summary_funs.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"><title>Check for List of Summary Functions — assert_summary_funs • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 List of Summary Functions — assert_summary_funs"><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>Check for List of Summary Functions — assert_summary_funs • teal.modules.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 List of Summary Functions — assert_summary_funs"><meta name="description" content="
 Check whether x is a list of summary functions."><meta property="og:description" content="
 Check whether x is a list of summary functions."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/assertion_arguments.html b/main/reference/assertion_arguments.html
index 2d14c076..ede57734 100644
--- a/main/reference/assertion_arguments.html
+++ b/main/reference/assertion_arguments.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"><title>Standard Assertion Arguments — assertion_arguments • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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
+<!-- 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 • teal.modules.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."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/assertions.html b/main/reference/assertions.html
index 7a7acfff..71abb142 100644
--- a/main/reference/assertions.html
+++ b/main/reference/assertions.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"><title>Additional Assertions for checkmate — assertions • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Additional Assertions for checkmate — assertions"><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>Additional Assertions for checkmate — assertions • teal.modules.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="Additional Assertions for checkmate — assertions"><meta name="description" content="
 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:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/check_reactive.html b/main/reference/check_reactive.html
index ecba1748..7a96c7c8 100644
--- a/main/reference/check_reactive.html
+++ b/main/reference/check_reactive.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"><title>Check for Reactive Input — check_reactive • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Reactive Input — check_reactive"><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>Check for Reactive Input — check_reactive • teal.modules.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 Reactive Input — check_reactive"><meta name="description" content="
 Check whether x is a reactive input."><meta property="og:description" content="
 Check whether x is a reactive input."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/check_tag.html b/main/reference/check_tag.html
index beab9828..d239bc7a 100644
--- a/main/reference/check_tag.html
+++ b/main/reference/check_tag.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"><title>Check for Shiny Tag — check_tag • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Shiny Tag — check_tag"><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>Check for Shiny Tag — check_tag • teal.modules.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 Shiny Tag — check_tag"><meta name="description" content="
 Check whether x is a shiny tag."><meta property="og:description" content="
 Check whether x is a shiny tag."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/experimentSpecInput.html b/main/reference/experimentSpecInput.html
index bf0897a6..e989282b 100644
--- a/main/reference/experimentSpecInput.html
+++ b/main/reference/experimentSpecInput.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"><title>Module Input for Experiment Specification — experimentSpecInput • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Input for Experiment Specification — experimentSpecInput"><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>Module Input for Experiment Specification — experimentSpecInput • teal.modules.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="Module Input for Experiment Specification — experimentSpecInput"><meta name="description" content="
 This defines the input for the experiment specification."><meta property="og:description" content="
 This defines the input for the experiment specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/experimentSpecServer.html b/main/reference/experimentSpecServer.html
index f4a41142..d019326e 100644
--- a/main/reference/experimentSpecServer.html
+++ b/main/reference/experimentSpecServer.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"><title>Module Server for Experiment Specification — experimentSpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for Experiment Specification — experimentSpecServer"><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>Module Server for Experiment Specification — experimentSpecServer • teal.modules.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="Module Server for Experiment Specification — experimentSpecServer"><meta name="description" content="
 This defines the server part for the experiment specification."><meta property="og:description" content="
 This defines the server part for the experiment specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -102,7 +92,7 @@ <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 following reactive objects:</p><ul><li><p><code>data</code>: the <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/HermesData-class.html" class="external-link">hermes::AnyHermesData</a></code> experiment.</p></li>
+    <p>List with the following reactive objects:</p><ul><li><p><code>data</code>: the <code><a href="https://rdrr.io/pkg/hermes/man/HermesData-class.html" class="external-link">hermes::AnyHermesData</a></code> experiment.</p></li>
 <li><p><code>name</code>: the name of the experiment as selected by the user.</p></li>
 <li><p><code>genes</code>: a <code>data.frame</code> with the genes in <code>data</code>, with columns <code>id</code> and <code>name</code>.</p></li>
 <li><p><code>assays</code>: the names of the assays in <code>data</code>.</p></li>
@@ -163,7 +153,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="va">output</span><span class="op">$</span><span class="va">summary</span> <span class="op">&lt;-</span> <span class="fu">renderPrint</span><span class="op">(</span><span class="op">{</span></span></span>
 <span class="r-in"><span>      <span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">result</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-in"><span>      <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span></span>
+<span class="r-in"><span>      <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="va">output</span><span class="op">$</span><span class="va">head</span> <span class="op">&lt;-</span> <span class="fu">renderPrint</span><span class="op">(</span><span class="op">{</span></span></span>
 <span class="r-in"><span>      <span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">result</span><span class="op">(</span><span class="op">)</span></span></span>
@@ -173,7 +163,7 @@ <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>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">my_app</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>    data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>    modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
diff --git a/main/reference/function_arguments.html b/main/reference/function_arguments.html
index 69eb6b17..90523b08 100644
--- a/main/reference/function_arguments.html
+++ b/main/reference/function_arguments.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"><title>Standard Function Arguments — function_arguments • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Function Arguments — function_arguments"><meta name="description" content="The documentation to this function lists all the conventional arguments in
+<!-- 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 Function Arguments — function_arguments • teal.modules.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 Function Arguments — function_arguments"><meta name="description" content="The documentation to this function lists all the conventional arguments in
 functions."><meta property="og:description" content="The documentation to this function lists all the conventional arguments in
 functions."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -72,7 +62,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 <dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> specification for gene(s) (signature), e.g.
-using <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">hermes::gene_spec()</a></code>.</p></dd>
+using <code><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">hermes::gene_spec()</a></code>.</p></dd>
 
 
 <dt id="arg-experiment-name">experiment_name<a class="anchor" aria-label="anchor" href="#arg-experiment-name"></a></dt>
diff --git a/main/reference/geneSpecInput.html b/main/reference/geneSpecInput.html
index bdfb04ba..ea82f1b5 100644
--- a/main/reference/geneSpecInput.html
+++ b/main/reference/geneSpecInput.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"><title>Module Input for Gene Signature Specification — geneSpecInput • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Input for Gene Signature Specification — geneSpecInput"><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>Module Input for Gene Signature Specification — geneSpecInput • teal.modules.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="Module Input for Gene Signature Specification — geneSpecInput"><meta name="description" content="
 This defines the input for the gene signature specification."><meta property="og:description" content="
 This defines the input for the gene signature specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/geneSpecServer.html b/main/reference/geneSpecServer.html
index 23cba1d2..3c480d89 100644
--- a/main/reference/geneSpecServer.html
+++ b/main/reference/geneSpecServer.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"><title>Module Server for Gene Signature Specification — geneSpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for Gene Signature Specification — geneSpecServer"><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>Module Server for Gene Signature Specification — geneSpecServer • teal.modules.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="Module Server for Gene Signature Specification — geneSpecServer"><meta name="description" content="
 This defines the server part for the gene signature specification."><meta property="og:description" content="
 This defines the server part for the gene signature specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -89,7 +79,7 @@ <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>Reactive <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/GeneSpec.html" class="external-link">hermes::GeneSpec</a></code> which can be used as input for the relevant
+    <p>Reactive <code><a href="https://rdrr.io/pkg/hermes/man/GeneSpec.html" class="external-link">hermes::GeneSpec</a></code> which can be used as input for the relevant
 <code>hermes</code> functions.</p>
     </div>
     <div class="section level2">
@@ -146,7 +136,7 @@ <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>
 <span class="r-in"><span><span class="va">funs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>mean <span class="op">=</span> <span class="va">colMeans</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">my_app</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>    data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>    modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
diff --git a/main/reference/h_assign_to_group_list.html b/main/reference/h_assign_to_group_list.html
index ca3ffe7a..ed87d2dc 100644
--- a/main/reference/h_assign_to_group_list.html
+++ b/main/reference/h_assign_to_group_list.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"><title>Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Group List Creation — h_assign_to_group_list"><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>Helper Function For Group List Creation — h_assign_to_group_list • teal.modules.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 Group List Creation — h_assign_to_group_list"><meta name="description" content="
 This helper function takes an assignment list and converts it to a
 group list."><meta property="og:description" content="
 This helper function takes an assignment list and converts it to a
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/h_collapse_levels.html b/main/reference/h_collapse_levels.html
index 3bc41c25..43e2b622 100644
--- a/main/reference/h_collapse_levels.html
+++ b/main/reference/h_collapse_levels.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"><title>Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Collapsing of Factor Levels — h_collapse_levels"><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>Helper Function for Collapsing of Factor Levels — h_collapse_levels • teal.modules.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 Collapsing of Factor Levels — h_collapse_levels"><meta name="description" content="
 Given a group list and a factor, this helper function collapses the
 levels in the factor accordingly and also ensures that the resulting
 levels are in the order given in the group list."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/h_extract_words.html b/main/reference/h_extract_words.html
index 390d5a3c..dcb8a238 100644
--- a/main/reference/h_extract_words.html
+++ b/main/reference/h_extract_words.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"><title>Helper Function to Extract Words — h_extract_words • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 to Extract Words — h_extract_words"><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>Helper Function to Extract Words — h_extract_words • teal.modules.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 to Extract Words — h_extract_words"><meta name="description" content="
 This helper function extracts words from a string. Here words are defined
 as containing lower or upper case letters, colons and dots. All other
 characters are considered separators."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/h_gene_data.html b/main/reference/h_gene_data.html
index 20f9382e..cddd256f 100644
--- a/main/reference/h_gene_data.html
+++ b/main/reference/h_gene_data.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"><title>Helper Function to Format Gene Choices — h_gene_data • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 to Format Gene Choices — h_gene_data"><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>Helper Function to Format Gene Choices — h_gene_data • teal.modules.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 to Format Gene Choices — h_gene_data"><meta name="description" content="
 Given a hermes::AnyHermesData data object, as well as the annotation
 column name to use as gene name, this function formats the contained genes
 as a data.frame ready for consumption in h_order_genes() e.g."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -50,7 +40,7 @@ <h1>Helper Function to Format Gene Choices</h1>
 
     <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>Given a <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/HermesData-class.html" class="external-link">hermes::AnyHermesData</a></code> data object, as well as the annotation
+<p>Given a <code><a href="https://rdrr.io/pkg/hermes/man/HermesData-class.html" class="external-link">hermes::AnyHermesData</a></code> data object, as well as the annotation
 column name to use as gene name, this function formats the contained genes
 as a <code>data.frame</code> ready for consumption in <code><a href="h_order_genes.html">h_order_genes()</a></code> e.g.</p>
     </div>
@@ -88,7 +78,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/hermes_data.html" class="external-link">hermes_data</a></span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span>, <span class="op">]</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/hermes_data.html" class="external-link">hermes_data</a></span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span><span class="fu">h_gene_data</span><span class="op">(</span><span class="va">object</span>, <span class="st">"symbol"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                  id         name</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1      GeneID:11185         INMT</span>
diff --git a/main/reference/h_km_mae_to_adtte.html b/main/reference/h_km_mae_to_adtte.html
index 628592e3..3e3eaf30 100644
--- a/main/reference/h_km_mae_to_adtte.html
+++ b/main/reference/h_km_mae_to_adtte.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"><title>Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Data Preprocessing for ADTTE Module — h_km_mae_to_adtte"><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>Data Preprocessing for ADTTE Module — h_km_mae_to_adtte • teal.modules.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="Data Preprocessing for ADTTE Module — h_km_mae_to_adtte"><meta name="description" content="
 A function to help with merging of MAE to ADTTE."><meta property="og:description" content="
 A function to help with merging of MAE to ADTTE."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -75,7 +65,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 <dt id="arg-genes">genes<a class="anchor" aria-label="anchor" href="#arg-genes"></a></dt>
 <dd><p>(<code>GeneSpec</code>)<br> specification for gene(s) (signature), e.g.
-using <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">hermes::gene_spec()</a></code>.</p></dd>
+using <code><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">hermes::gene_spec()</a></code>.</p></dd>
 
 
 <dt id="arg-experiment-name">experiment_name<a class="anchor" aria-label="anchor" href="#arg-experiment-name"></a></dt>
@@ -106,26 +96,26 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">mae</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
+<span class="r-in"><span><span class="va">mae</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
 <span class="r-in"><span><span class="va">adtte</span> <span class="op">&lt;-</span> <span class="fu">teal.modules.hermes</span><span class="fu">::</span><span class="va"><a href="rADTTE.html">rADTTE</a></span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>CNSR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/logical.html" class="external-link">as.logical</a></span><span class="op">(</span><span class="va">CNSR</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">new_adtte</span> <span class="op">&lt;-</span> <span class="fu">h_km_mae_to_adtte</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="va">adtte</span>,</span></span>
 <span class="r-in"><span>  <span class="va">mae</span>,</span></span>
-<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">gene_spec</a></span><span class="op">(</span><span class="st">"GeneID:1820"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">gene_spec</a></span><span class="op">(</span><span class="st">"GeneID:1820"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  experiment_name <span class="op">=</span> <span class="st">"hd2"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">new_adtte2</span> <span class="op">&lt;-</span> <span class="fu">h_km_mae_to_adtte</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="va">adtte</span>,</span></span>
 <span class="r-in"><span>  <span class="va">mae</span>,</span></span>
-<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">gene_spec</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="st">"GeneID:1820"</span>, <span class="st">"GeneID:94115"</span><span class="op">)</span>, fun <span class="op">=</span> <span class="va">colMeans</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">gene_spec</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="st">"GeneID:1820"</span>, <span class="st">"GeneID:94115"</span><span class="op">)</span>, fun <span class="op">=</span> <span class="va">colMeans</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  experiment_name <span class="op">=</span> <span class="st">"hd2"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">new_adtte3</span> <span class="op">&lt;-</span> <span class="fu">h_km_mae_to_adtte</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="va">adtte</span>,</span></span>
 <span class="r-in"><span>  <span class="va">mae</span>,</span></span>
-<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">gene_spec</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>A <span class="op">=</span> <span class="st">"GeneID:1820"</span>, B <span class="op">=</span> <span class="st">"GeneID:94115"</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">gene_spec</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>A <span class="op">=</span> <span class="st">"GeneID:1820"</span>, B <span class="op">=</span> <span class="st">"GeneID:94115"</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  experiment_name <span class="op">=</span> <span class="st">"hd2"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 </code></pre></div>
diff --git a/main/reference/h_order_genes.html b/main/reference/h_order_genes.html
index 2200e897..55f74f94 100644
--- a/main/reference/h_order_genes.html
+++ b/main/reference/h_order_genes.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"><title>Helper Function to Order Gene Choices — h_order_genes • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 to Order Gene Choices — h_order_genes"><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>Helper Function to Order Gene Choices — h_order_genes • teal.modules.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 to Order Gene Choices — h_order_genes"><meta name="description" content="
 The possible gene choices are ordered as follows. First come all genes which
 have a non-empty name, ordered by their name alphabetically. Last come
 all genes with an empty name, ordered by their ID alphabetically."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/h_parse_genes.html b/main/reference/h_parse_genes.html
index 7479b2c6..49dacc82 100644
--- a/main/reference/h_parse_genes.html
+++ b/main/reference/h_parse_genes.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"><title>Helper Function to Parse Genes — h_parse_genes • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 to Parse Genes — h_parse_genes"><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>Helper Function to Parse Genes — h_parse_genes • teal.modules.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 to Parse Genes — h_parse_genes"><meta name="description" content="
 This helper function takes a vector of words and tries to match them
 with the id and name columns of possible gene choices."><meta property="og:description" content="
 This helper function takes a vector of words and tries to match them
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/h_update_gene_selection.html b/main/reference/h_update_gene_selection.html
index dfd75ef4..afe8aca6 100644
--- a/main/reference/h_update_gene_selection.html
+++ b/main/reference/h_update_gene_selection.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"><title>Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 to Update Gene Selection — h_update_gene_selection"><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>Helper Function to Update Gene Selection — h_update_gene_selection • teal.modules.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 to Update Gene Selection — h_update_gene_selection"><meta name="description" content="
 This helper function takes the intersection of selected and
 choices for genes and updates the inputId accordingly. It then
 shows a notification if not all selected genes were available."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/heatmap_plot.html b/main/reference/heatmap_plot.html
index 72baf305..df4ccb5b 100644
--- a/main/reference/heatmap_plot.html
+++ b/main/reference/heatmap_plot.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"><title>Correlation Heatmap Plot — heatmap_plot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Heatmap Plot — heatmap_plot"><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 Heatmap Plot — heatmap_plot • teal.modules.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 Heatmap Plot — heatmap_plot"><meta name="description" content="
 This function plots the correlation heatmap."><meta property="og:description" content="
 This function plots the correlation heatmap."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -73,7 +63,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://insightsengineering.github.io/hermes/" class="external-link">hermes</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/insightsengineering/hermes/" class="external-link">hermes</a></span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: ggfortify</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: SummarizedExperiment</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: MatrixGenerics</span>
@@ -119,8 +109,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     as.data.frame, basename, cbind, colnames, dirname, do.call,</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>     union, unique, unsplit, which.max, which.min</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>     tapply, union, unique, unsplit, which.max, which.min</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: S4Vectors</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘S4Vectors’</span>
@@ -162,7 +152,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> The following object is masked from ‘package:stats’:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     filter</span>
-<span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">(</span><span class="va">summarized_experiment</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/hermes/man/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">(</span><span class="va">summarized_experiment</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">heatmap_plot</span><span class="op">(</span><span class="va">object</span>, assay_name <span class="op">=</span> <span class="st">"counts"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
diff --git a/main/reference/include_css_files.html b/main/reference/include_css_files.html
index b891b7bf..53b1b27e 100644
--- a/main/reference/include_css_files.html
+++ b/main/reference/include_css_files.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"><title>Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Include CSS files from /inst/css/ package directory to application header — include_css_files"><meta name="description" content="system.file should not be used to access files in other packages, it does
+<!-- 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>Include CSS files from /inst/css/ package directory to application header — include_css_files • teal.modules.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="Include CSS files from /inst/css/ package directory to application header — include_css_files"><meta name="description" content="system.file should not be used to access files in other packages, it does
 not work with devtools. Therefore, we redefine this method in each package
 as needed. Thus, we do not export this method"><meta property="og:description" content="system.file should not be used to access files in other packages, it does
 not work with devtools. Therefore, we redefine this method in each package
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/include_js_files.html b/main/reference/include_js_files.html
index da0d2a7b..caea14f7 100644
--- a/main/reference/include_js_files.html
+++ b/main/reference/include_js_files.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"><title>Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Include JS files from /inst/js/ package directory to application header — include_js_files"><meta name="description" content="system.file should not be used to access files in other packages, it does
+<!-- 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>Include JS files from /inst/js/ package directory to application header — include_js_files • teal.modules.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="Include JS files from /inst/js/ package directory to application header — include_js_files"><meta name="description" content="system.file should not be used to access files in other packages, it does
 not work with devtools. Therefore, we redefine this method in each package
 as needed. Thus, we do not export this method"><meta property="og:description" content="system.file should not be used to access files in other packages, it does
 not work with devtools. Therefore, we redefine this method in each package
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/index.html b/main/reference/index.html
index 8127f78e..35c9aa24 100644
--- a/main/reference/index.html
+++ b/main/reference/index.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"><title>Package index • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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 • teal.modules.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"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
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-        <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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
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diff --git a/main/reference/is_blank.html b/main/reference/is_blank.html
index 3a9491c9..459f31ca 100644
--- a/main/reference/is_blank.html
+++ b/main/reference/is_blank.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"><title>Checking for Empty String — is_blank • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 String — is_blank"><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>Checking for Empty String — is_blank • teal.modules.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 String — is_blank"><meta name="description" content="
 This predicate function is helpful for functions where arguments could
 not yet be initialized from the teal module."><meta property="og:description" content="
 This predicate function is helpful for functions where arguments could
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</a></li>
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-        <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/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
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diff --git a/main/reference/module_arguments.html b/main/reference/module_arguments.html
index c44a71cb..b415e319 100644
--- a/main/reference/module_arguments.html
+++ b/main/reference/module_arguments.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"><title>Standard Module Arguments — module_arguments • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Module Arguments — module_arguments"><meta name="description" content="The documentation to this function lists all the conventional arguments in
+<!-- 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 Module Arguments — module_arguments • teal.modules.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 Module Arguments — module_arguments"><meta name="description" content="The documentation to this function lists all the conventional arguments in
 hermes teal modules."><meta property="og:description" content="The documentation to this function lists all the conventional arguments in
 hermes teal modules."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</a></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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-        <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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
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diff --git a/main/reference/multiSampleVarSpecServer.html b/main/reference/multiSampleVarSpecServer.html
index 8d0c124e..5801b56d 100644
--- a/main/reference/multiSampleVarSpecServer.html
+++ b/main/reference/multiSampleVarSpecServer.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"><title>Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer"><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>Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer • teal.modules.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="Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer"><meta name="description" content="
 When multiple sample variables are used in a given module, then this
 wrapper makes it much easier to specify in the server function."><meta property="og:description" content="
 When multiple sample variables are used in a given module, then this
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</a></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
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diff --git a/main/reference/rADTTE.html b/main/reference/rADTTE.html
index 4a92a730..01b17b31 100644
--- a/main/reference/rADTTE.html
+++ b/main/reference/rADTTE.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"><title>Random Time to Event Analysis Dataset — rADTTE • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Random Time to Event Analysis Dataset — rADTTE"><meta name="description" content="Random Time to Event Analysis Dataset"><meta property="og:description" content="Random Time to Event Analysis Dataset"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
+<!-- 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>Random Time to Event Analysis Dataset — rADTTE • teal.modules.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="Random Time to Event Analysis Dataset — rADTTE"><meta name="description" content="Random Time to Event Analysis Dataset"><meta property="og:description" content="Random Time to Event Analysis Dataset"><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -19,16 +19,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/sampleVarSpecInput.html b/main/reference/sampleVarSpecInput.html
index fea6efd0..26375273 100644
--- a/main/reference/sampleVarSpecInput.html
+++ b/main/reference/sampleVarSpecInput.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"><title>Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Input for Sample Variable Specification — sampleVarSpecInput"><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>Module Input for Sample Variable Specification — sampleVarSpecInput • teal.modules.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="Module Input for Sample Variable Specification — sampleVarSpecInput"><meta name="description" content="
 This defines the input for the sample variable specification."><meta property="og:description" content="
 This defines the input for the sample variable specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/sampleVarSpecServer.html b/main/reference/sampleVarSpecServer.html
index 3ba409d0..0b3c79dc 100644
--- a/main/reference/sampleVarSpecServer.html
+++ b/main/reference/sampleVarSpecServer.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"><title>Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Module Server for Sample Variable Specification — sampleVarSpecServer"><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>Module Server for Sample Variable Specification — sampleVarSpecServer • teal.modules.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="Module Server for Sample Variable Specification — sampleVarSpecServer"><meta name="description" content="
 This defines the server part for the sample variable specification."><meta property="og:description" content="
 This defines the server part for the sample variable specification."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -104,7 +94,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 <dt id="arg-explicit-na">explicit_na<a class="anchor" aria-label="anchor" href="#arg-explicit-na"></a></dt>
 <dd><p>(<code>flag</code>)<br> whether the <code>colData</code> of <code>original_data</code> will be transformed with
-<a href="https://insightsengineering.github.io/hermes/latest-tag/reference/h_df_factors_with_explicit_na.html" class="external-link">hermes::h_df_factors_with_explicit_na</a> before further processing. That means also that
+<a href="https://rdrr.io/pkg/hermes/man/h_df_factors_with_explicit_na.html" class="external-link">hermes::h_df_factors_with_explicit_na</a> before further processing. That means also that
 <code>NA</code> will be made an explicit factor level and counted for <code>num_levels</code>.</p></dd>
 
 
@@ -114,7 +104,7 @@ <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>Reactive <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> which can be used as
+    <p>Reactive <code><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">SummarizedExperiment::SummarizedExperiment</a></code> which can be used as
 input for the relevant <code>hermes</code> functions.</p>
     </div>
     <div class="section level2">
@@ -157,7 +147,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>      <span class="va">mae</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="op">)</span><span class="op">[[</span><span class="st">"MAE"</span><span class="op">]</span><span class="op">]</span></span></span>
 <span class="r-in"><span>      <span class="va">object</span> <span class="op">&lt;-</span> <span class="va">mae</span><span class="op">[[</span><span class="va">input</span><span class="op">$</span><span class="va">experiment_name</span><span class="op">]</span><span class="op">]</span></span></span>
 <span class="r-in"><span>      <span class="fu">SummarizedExperiment</span><span class="fu">::</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></span>
-<span class="r-in"><span>        <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/df_cols_to_factor.html" class="external-link">df_cols_to_factor</a></span><span class="op">(</span><span class="fu">SummarizedExperiment</span><span class="fu">::</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="r-in"><span>        <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/df_cols_to_factor.html" class="external-link">df_cols_to_factor</a></span><span class="op">(</span><span class="fu">SummarizedExperiment</span><span class="fu">::</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="r-in"><span>      <span class="va">object</span></span></span>
 <span class="r-in"><span>    <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="va">facet_var_spec</span> <span class="op">&lt;-</span> <span class="fu">sampleVarSpecServer</span><span class="op">(</span></span></span>
@@ -170,17 +160,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="va">output</span><span class="op">$</span><span class="va">plot</span> <span class="op">&lt;-</span> <span class="fu">renderPlot</span><span class="op">(</span><span class="op">{</span></span></span>
 <span class="r-in"><span>      <span class="va">experiment_data_final</span> <span class="op">&lt;-</span> <span class="va">facet_var_spec</span><span class="op">$</span><span class="fu">experiment_data</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span>      <span class="va">facet_var</span> <span class="op">&lt;-</span> <span class="va">facet_var_spec</span><span class="op">$</span><span class="fu">sample_var</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-in"><span>      <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/draw_boxplot.html" class="external-link">draw_boxplot</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>      <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/draw_boxplot.html" class="external-link">draw_boxplot</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>        <span class="va">experiment_data_final</span>,</span></span>
 <span class="r-in"><span>        assay_name <span class="op">=</span> <span class="st">"counts"</span>,</span></span>
-<span class="r-in"><span>        genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/gene_spec.html" class="external-link">gene_spec</a></span><span class="op">(</span><span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/genes.html" class="external-link">genes</a></span><span class="op">(</span><span class="va">experiment_data_final</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>        genes <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/gene_spec.html" class="external-link">gene_spec</a></span><span class="op">(</span><span class="fu">hermes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/hermes/man/genes.html" class="external-link">genes</a></span><span class="op">(</span><span class="va">experiment_data_final</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>        facet_var <span class="op">=</span> <span class="va">facet_var</span></span></span>
 <span class="r-in"><span>      <span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-in"><span><span class="va">my_app</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>    data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>    modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
diff --git a/main/reference/teal.modules.hermes-package.html b/main/reference/teal.modules.hermes-package.html
index 6ab1ded6..372a23ce 100644
--- a/main/reference/teal.modules.hermes-package.html
+++ b/main/reference/teal.modules.hermes-package.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"><title>teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="teal.modules.hermes Package — teal.modules.hermes-package"><meta name="description" content="teal.modules.hermes provides RNA-seq analysis modules to add to a
+<!-- 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>teal.modules.hermes Package — teal.modules.hermes-package • teal.modules.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="teal.modules.hermes Package — teal.modules.hermes-package"><meta name="description" content="teal.modules.hermes provides RNA-seq analysis modules to add to a
 teal application."><meta property="og:description" content="teal.modules.hermes provides RNA-seq analysis modules to add to a
 teal application."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/reference/tm_g_barplot.html b/main/reference/tm_g_barplot.html
index 4cdd30e7..36accd87 100644
--- a/main/reference/tm_g_barplot.html
+++ b/main/reference/tm_g_barplot.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"><title>Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for RNA-seq Barplot — tm_g_barplot"><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>Teal Module for RNA-seq Barplot — tm_g_barplot • teal.modules.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="Teal Module for RNA-seq Barplot — tm_g_barplot"><meta name="description" content="
 This module provides an interactive barplot for RNA-seq gene expression
 analysis."><meta property="og:description" content="
 This module provides an interactive barplot for RNA-seq gene expression
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -159,7 +149,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -170,7 +160,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_barplot</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_boxplot.html b/main/reference/tm_g_boxplot.html
index 64d24ef2..aff5f6aa 100644
--- a/main/reference/tm_g_boxplot.html
+++ b/main/reference/tm_g_boxplot.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"><title>Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for RNA-seq Boxplot — tm_g_boxplot"><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>Teal Module for RNA-seq Boxplot — tm_g_boxplot • teal.modules.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="Teal Module for RNA-seq Boxplot — tm_g_boxplot"><meta name="description" content="
 This module provides an interactive boxplot for RNA-seq gene expression
 analysis."><meta property="og:description" content="
 This module provides an interactive boxplot for RNA-seq gene expression
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -159,7 +149,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -170,7 +160,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_boxplot</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_forest_tte.html b/main/reference/tm_g_forest_tte.html
index f37503b0..a243375f 100644
--- a/main/reference/tm_g_forest_tte.html
+++ b/main/reference/tm_g_forest_tte.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"><title>Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for Survival Forest Plot — tm_g_forest_tte"><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>Teal Module for Survival Forest Plot — tm_g_forest_tte • teal.modules.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="Teal Module for Survival Forest Plot — tm_g_forest_tte"><meta name="description" content="
 This module provides an interactive survival forest plot."><meta property="og:description" content="
 This module provides an interactive survival forest plot."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -200,7 +190,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">within</a></span><span class="op">(</span><span class="va">data</span>, <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">ADTTE</span> <span class="op">&lt;-</span> <span class="fu">teal.modules.hermes</span><span class="fu">::</span><span class="va"><a href="rADTTE.html">rADTTE</a></span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>is_event <span class="op">=</span> <span class="va">.data</span><span class="op">$</span><span class="va">CNSR</span> <span class="op">==</span> <span class="fl">0</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
+<span class="r-in"><span>  <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
 <span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">datanames</span> <span class="op">&lt;-</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">"ADTTE"</span>, <span class="st">"MAE"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">datanames</span><span class="op">(</span><span class="va">data</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datanames</span></span></span>
@@ -217,7 +207,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_forest_tte</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_km.html b/main/reference/tm_g_km.html
index 222ce80a..528099c7 100644
--- a/main/reference/tm_g_km.html
+++ b/main/reference/tm_g_km.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"><title>Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for Kaplan-Meier Plot — tm_g_km"><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>Teal Module for Kaplan-Meier Plot — tm_g_km • teal.modules.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="Teal Module for Kaplan-Meier Plot — tm_g_km"><meta name="description" content="
 This teal module produces a grid style Kaplan-Meier plot for data with
 ADaM structure."><meta property="og:description" content="
 This teal module produces a grid style Kaplan-Meier plot for data with
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -189,7 +179,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">within</a></span><span class="op">(</span><span class="va">data</span>, <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">ADTTE</span> <span class="op">&lt;-</span> <span class="fu">teal.modules.hermes</span><span class="fu">::</span><span class="va"><a href="rADTTE.html">rADTTE</a></span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>is_event <span class="op">=</span> <span class="va">.data</span><span class="op">$</span><span class="va">CNSR</span> <span class="op">==</span> <span class="fl">0</span><span class="op">)</span></span></span>
-<span class="r-in"><span>  <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
+<span class="r-in"><span>  <span class="va">MAE</span> <span class="op">&lt;-</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span></span></span>
 <span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">datanames</span> <span class="op">&lt;-</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">"ADTTE"</span>, <span class="st">"MAE"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">datanames</span><span class="op">(</span><span class="va">data</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datanames</span></span></span>
@@ -209,7 +199,6 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="va">modules</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span>ui <span class="op">=</span> <span class="va">app</span><span class="op">$</span><span class="va">ui</span>, server <span class="op">=</span> <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
diff --git a/main/reference/tm_g_pca.html b/main/reference/tm_g_pca.html
index 1dd55280..0f70736d 100644
--- a/main/reference/tm_g_pca.html
+++ b/main/reference/tm_g_pca.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"><title>Teal Module for PCA Analysis — tm_g_pca • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for PCA Analysis — tm_g_pca"><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>Teal Module for PCA Analysis — tm_g_pca • teal.modules.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="Teal Module for PCA Analysis — tm_g_pca"><meta name="description" content="
 This module provides an interactive principal components plot and an
 interactive heatmap with correlation of principal components with sample
 variables."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -146,7 +136,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -157,7 +147,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_pca</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_quality.html b/main/reference/tm_g_quality.html
index 090cde0c..4a14330a 100644
--- a/main/reference/tm_g_quality.html
+++ b/main/reference/tm_g_quality.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"><title>Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for RNA-seq Quality Control — tm_g_quality"><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>Teal Module for RNA-seq Quality Control — tm_g_quality • teal.modules.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="Teal Module for RNA-seq Quality Control — tm_g_quality"><meta name="description" content="
 This module adds quality flags, filters by genes and/or samples,
 normalizes AnyHermesData objects and provides interactive plots
 for RNA-seq gene expression quality control."><meta property="og:description" content="
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,16 +25,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -146,7 +136,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -156,7 +146,6 @@ <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>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_scatterplot.html b/main/reference/tm_g_scatterplot.html
index a4184d9c..5d9e7b48 100644
--- a/main/reference/tm_g_scatterplot.html
+++ b/main/reference/tm_g_scatterplot.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"><title>Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for RNA-seq Scatterplot — tm_g_scatterplot"><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>Teal Module for RNA-seq Scatterplot — tm_g_scatterplot • teal.modules.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="Teal Module for RNA-seq Scatterplot — tm_g_scatterplot"><meta name="description" content="
 This module provides an interactive scatterplot for RNA-seq gene expression
 analysis."><meta property="og:description" content="
 This module provides an interactive scatterplot for RNA-seq gene expression
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -159,7 +149,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -170,7 +160,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_scatterplot</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_volcanoplot.html b/main/reference/tm_g_volcanoplot.html
index c6a74d76..00854da2 100644
--- a/main/reference/tm_g_volcanoplot.html
+++ b/main/reference/tm_g_volcanoplot.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"><title>Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot"><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>Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot • teal.modules.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="Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot"><meta name="description" content="
 This module provides an interactive volcano plot for RNA-seq gene expression
 analysis."><meta property="og:description" content="
 This module provides an interactive volcano plot for RNA-seq gene expression
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -143,7 +133,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu">teal_data</span><span class="op">(</span>MAE <span class="op">=</span> <span class="fu">hermes</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/hermes/man/multi_assay_experiment.html" class="external-link">multi_assay_experiment</a></span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
 <span class="r-in"><span>  modules <span class="op">=</span> <span class="fu">modules</span><span class="op">(</span></span></span>
@@ -154,7 +144,6 @@ <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>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing tm_g_volcanoplot</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Initializing reporter_previewer_module</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/top_gene_plot.html b/main/reference/top_gene_plot.html
index f0fd3bfc..dc5b285c 100644
--- a/main/reference/top_gene_plot.html
+++ b/main/reference/top_gene_plot.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"><title>Most Expressed Genes Plot — top_gene_plot • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Most Expressed Genes Plot — top_gene_plot"><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>Most Expressed Genes Plot — top_gene_plot • teal.modules.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="Most Expressed Genes Plot — top_gene_plot"><meta name="description" content="
 This function plots the most expressed genes."><meta property="og:description" content="
 This function plots the most expressed genes."><link rel="stylesheet" href="../consent.css"><script src="../consent.js" type="text/javascript" charset="utf-8"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -21,16 +21,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -73,8 +63,8 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://insightsengineering.github.io/hermes/" class="external-link">hermes</a></span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">(</span><span class="va">summarized_experiment</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/insightsengineering/hermes/" class="external-link">hermes</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/hermes/man/HermesData-class.html" class="external-link">HermesData</a></span><span class="op">(</span><span class="va">summarized_experiment</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">top_gene_plot</span><span class="op">(</span><span class="va">object</span>, assay_name <span class="op">=</span> <span class="st">"counts"</span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
diff --git a/main/reference/validate_gene_spec.html b/main/reference/validate_gene_spec.html
index 13f39c6a..d943afed 100644
--- a/main/reference/validate_gene_spec.html
+++ b/main/reference/validate_gene_spec.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"><title>Validation of Gene Specification — validate_gene_spec • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Validation of Gene Specification — validate_gene_spec"><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>Validation of Gene Specification — validate_gene_spec • teal.modules.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="Validation of Gene Specification — validate_gene_spec"><meta name="description" content="
 This validation function checks that a given hermes::GeneSpec has at least
 one gene selected and that all genes are included in possible choices."><meta property="og:description" content="
 This validation function checks that a given hermes::GeneSpec has at least
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
@@ -48,7 +38,7 @@ <h1>Validation of Gene Specification</h1>
 
     <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 validation function checks that a given <code><a href="https://insightsengineering.github.io/hermes/latest-tag/reference/GeneSpec.html" class="external-link">hermes::GeneSpec</a></code> has at least
+<p>This validation function checks that a given <code><a href="https://rdrr.io/pkg/hermes/man/GeneSpec.html" class="external-link">hermes::GeneSpec</a></code> has at least
 one gene selected and that all genes are included in possible choices.</p>
     </div>
 
diff --git a/main/reference/validate_n_levels.html b/main/reference/validate_n_levels.html
index 2757c522..fda60cfe 100644
--- a/main/reference/validate_n_levels.html
+++ b/main/reference/validate_n_levels.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"><title>Validation of Number of Levels — validate_n_levels • teal.modules.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-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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="Validation of Number of Levels — validate_n_levels"><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>Validation of Number of Levels — validate_n_levels • teal.modules.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="Validation of Number of Levels — validate_n_levels"><meta name="description" content="
 This validation function checks that a given vector x is a factor with
 the specified number of levels."><meta property="og:description" content="
 This validation function checks that a given vector x is a factor with
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.6.9024</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -23,16 +23,6 @@
 <li class="nav-item"><a class="nav-link" href="../articles/index.html">Articles</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/teal.modules.hermes"><span class="fa fa-github"></span></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/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.6">v0.1.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul></div>
 
 
diff --git a/main/search.json b/main/search.json
index 08bd8baf..333aa7f6 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.hermes/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.hermes/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id, mae_name) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = plotOutput(ns(\"awesome_plot\"))   ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input,                 output,                 session,                 data,                 filter_panel_api,                 mae_name) {   output$encoding_ui <- renderUI({     tags$div(       experimentSpecInput(session$ns(\"experiment\"), data, mae_name),       assaySpecInput(session$ns(\"assay\"))     )   })   experiment <- experimentSpecServer(     \"experiment\",     data = data,     filter_panel_api = filter_panel_api,     mae_name = mae_name,     name_annotation = NULL # If you have a gene name column in your rowData, can specify here.   )   assay <- assaySpecServer(\"assay\", experiment$assays)   output$awesome_plot <- renderPlot({     data <- experiment$data()     assay <- assay()     req(assay %in% SummarizedExperiment::assayNames(data))     counts <- SummarizedExperiment::assay(data, assay)     df <- data.frame(gene = rownames(counts), counts = rowSums(counts))     df <- na.omit(df[order(df$counts, decreasing = TRUE), ])     df$gene <- factor(df$gene, levels = df$gene)     df <- df[1:10, ]     ggplot(df, aes(x = gene, y = counts)) +       geom_col() +       theme(axis.text.x = element_text(angle = 90))   }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") {   mae_name <- \"MAE\"   data <- teal_data(MAE = hermes::lapply(mae, hermes::HermesData))   app <- init(     data = data,     modules = teal::modules(       module(         label = label,         server = srv,         server_args = list(mae_name = mae_name),         ui = ui,         ui_args = list(mae_name = mae_name),         datanames = mae_name       )     )   )   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dony Unardi. Maintainer. Daniel Sabanés Bové. Author. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. Vedha Viyash. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.6.9023, https://github.com/insightsengineering/teal.modules.hermes/, https://insightsengineering.github.io/teal.modules.hermes/main/.","code":"@Manual{,   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},   year = {2024},   note = {R package version 0.1.6.9023,     https://github.com/insightsengineering/teal.modules.hermes/},   url = {https://insightsengineering.github.io/teal.modules.hermes/main/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes@*release\")  # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer(   id,   data,   mae_name,   adtte_name,   adtte_vars,   experiment_data,   experiment_name,   assay,   genes,   probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  ui <- function(id) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = verbatimTextOutput(ns(\"summary\"))   ) }  server <- function(id, data, filter_panel_api) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(session$ns(\"experiment\"), data, mae_name = \"MAE\"),         assaySpecInput(session$ns(\"assay\")),         geneSpecInput(session$ns(\"genes\"), funs = list(Mean = colMeans)),         adtteSpecInput(session$ns(\"adtte\"))       )     })     experiment <- experimentSpecServer(       \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       assays = experiment$assays     )     genes <- geneSpecServer(       \"genes\",       funs = list(Mean = colMeans),       gene_choices = experiment$genes     )     adtte <- adtteSpecServer(       \"adtte\",       data = data,       adtte_name = \"ADTTE\",       mae_name = \"MAE\",       adtte_vars = list(         aval = \"AVAL\",         avalu = \"AVALU\",         is_event = \"is_event\",         paramcd = \"PARAMCD\",         usubjid = \"USUBJID\"       ),       experiment_data = experiment$data,       experiment_name = experiment$name,       assay = assay,       genes = genes,       probs = reactive({         0.5       })     )     output$summary <- renderPrint({       binned_adtte_subset <- adtte$binned_adtte_subset()       summary(binned_adtte_subset)     })   }) }  my_app <- function() {   data <- teal_data()   data <- within(data, {     ADSL <- teal.data::rADSL     ADTTE <- teal.modules.hermes::rADTTE %>%       dplyr::mutate(is_event = .data$CNSR == 0)     MAE <- hermes::multi_assay_experiment   })   datanames <- c(\"ADSL\", \"ADTTE\", \"MAE\")   datanames(data) <- datanames   join_keys(data) <- default_cdisc_join_keys[datanames]    app <- init(     data = data,     modules = modules(       module(         label = \"adtteSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) }  if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = textOutput(ns(\"result\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, module = function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(session$ns(\"experiment\"), data, \"MAE\"),         assaySpecInput(           session$ns(\"assay\"),           label_assays = \"Please choose assay\"         )       )     })     experiment <- experimentSpecServer(       id = \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       experiment$assays,       exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\")     )     output$result <- renderPrint({       assay()     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"assaySpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.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/teal.modules.hermes/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — 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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x)  assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)  test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE)  assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)  test_tag(x, null.ok = FALSE)  expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput(   inputId,   data,   mae_name,   label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer(   id,   data,   filter_panel_api,   mae_name,   name_annotation = \"symbol\",   sample_vars_as_factors = TRUE,   with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id,                mae_name) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = tags$div(       verbatimTextOutput(ns(\"summary\")),       verbatimTextOutput(ns(\"head\"))     )   ) }  server <- function(id,                    data,                    filter_panel_api,                    mae_name) {   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(           session$ns(\"my_experiment\"),           data,           mae_name,           label_experiments = \"Please choose experiment\"         ),         selectInput(           session$ns(\"property\"),           \"Please choose property\",           c(\"data\", \"name\", \"genes\", \"assays\")         )       )     })     experiment <- experimentSpecServer(       \"my_experiment\",       data,       filter_panel_api,       mae_name     )     result <- reactive({       req(input$property)       switch(input$property,         data = experiment$data(),         name = experiment$name(),         genes = experiment$genes(),         assays = experiment$assays()       )     })     output$summary <- renderPrint({       result <- result()       hermes::summary(result)     })     output$head <- renderPrint({       result <- result()       utils::head(result)     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"experimentSpec example\",         server = server,         server_args = list(mae_name = \"MAE\"),         ui = ui,         ui_args = list(mae_name = \"MAE\"),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(   inputId,   funs,   label_genes = \"Select Gene(s)\",   label_funs = \"Select Gene Summary\",   label_text_button = \"Enter list of genes\",   label_lock_button =     \"Lock gene selection (so that it does not get updated when filtering)\",   label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"),   label_select_none_button = \"Select None\",   max_options = 200L,   max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select Gene(s)<\/label> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_none_button\" title=\"Select None\" type=\"button\"> #>       <span> #>         <i aria-label=\"remove-circle icon\" class=\"glyphicon glyphicon-remove-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_all_button\" title=\"Select All Genes (first 200)\" type=\"button\"> #>       <span> #>         <i aria-label=\"ok-circle icon\" class=\"glyphicon glyphicon-ok-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-text_button\" title=\"Enter list of genes\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-font\" role=\"presentation\" aria-label=\"font icon\"><\/i> #>       <\/span> #>     <\/button> #>     <div class=\"pull-right\" title=\"Lock gene selection (so that it does not get updated when filtering)\"> #>       <div class=\"form-group shiny-input-container\"> #>         <div class=\"pretty p-toggle p-plain p-icon p-pulse\"> #>           <input id=\"my_genes-lock_button\" type=\"checkbox\"/> #>           <div class=\"state p-on\"> #>             <i aria-label=\"lock icon\" class=\"fas fa-lock icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>           <div class=\"state p-off\"> #>             <i aria-label=\"lock-open icon\" class=\"fas fa-lock-open icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>         <\/div> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label shiny-label-null\" for=\"my_genes-genes\" id=\"my_genes-genes-label\"><\/label> #>     <div> #>       <select class=\"shiny-input-select form-control\" id=\"my_genes-genes\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-genes\" data-eval=\"[&quot;render&quot;]\">{\"placeholder\":\"- Nothing selected -\",\"render\":\"{\\n          option: function(item, escape) {\\n              return '<div> <span style=\\\"font-size: inherit;\\\">' + item.label + '<\\/div>' +\\n                ' <span style=\\\"color: #808080; font-size: xx-small;\\\" >' + item.value + '<\\/div> <\\/div>'\\n            }\\n          }\",\"searchField\":[\"value\",\"label\"],\"maxOptions\":200,\"maxItems\":200,\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"shiny-panel-conditional\" data-display-if=\"input.genes &amp;&amp; input.genes.length &gt; 1\" data-ns-prefix=\"my_genes-\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label\" id=\"my_genes-fun_name-label\" for=\"my_genes-fun_name\">Please select function<\/label> #>     <div> #>       <select id=\"my_genes-fun_name\" class=\"shiny-input-select\"><option value=\"mean\" selected>mean<\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-fun_name\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Gene Signature Specification — geneSpecServer","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"defines server part gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"geneSpecServer(   id,   funs,   gene_choices,   label_modal_title = \"Enter list of genes\",   label_modal_footer = c(\"Please enter a comma-separated list of gene IDs and/or names.\",     \"(Note that genes not included in current choices will be removed)\") )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"id (string) shiny module id. funs (static named list) names list used function selection drop menu. gene_choices (reactive data.frame) returns possible gene choices populate UI, data.frame columns id name. label_modal_title (string) title dialog asks text input. label_modal_footer (character) lines text use footer dialog.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"Reactive hermes::GeneSpec can used input relevant hermes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"ui <- function(id, funs) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = tags$div(       geneSpecInput(         ns(\"my_genes\"),         funs = funs,         label_funs = \"Please select function\"       )     ),     output = textOutput(ns(\"result\"))   ) } server <- function(id,                    data,                    funs) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     gene_choices <- reactive({       mae <- data()[[\"MAE\"]]       object <- mae[[1]]       gene_ids <- rownames(object)       gene_names <- SummarizedExperiment::rowData(object)$symbol       gene_data <- data.frame(         id = gene_ids,         name = gene_names       )       gene_data[order(gene_data$name), ]     })     gene_spec <- geneSpecServer(       \"my_genes\",       funs = funs,       gene_choices = gene_choices     )     output$result <- renderText({       validate_gene_spec(         gene_spec(),         gene_choices()$id       )       gene_spec <- gene_spec()       gene_spec$get_label()     })   }) } funs <- list(mean = colMeans) my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"GeneSpec example\",         server = server,         server_args = list(funs = funs),         ui = ui,         ui_args = list(funs = funs),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Group List Creation — h_assign_to_group_list","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"helper function takes assignment list converts group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"h_assign_to_group_list(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"x (named list character) input assignment list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"combination list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"assign_list <- list(   \"ASIAN\" = \"1\",   \"BLACK OR AFRICAN AMERICAN\" = \"1\",   \"MULTIPLE\" = \"2\",   \"UNKNOWN\" = \"2\",   \"WHITE\" = \"4\" ) objective_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) result_list <- h_assign_to_group_list(assign_list) stopifnot(identical(result_list, objective_list))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"Given group list factor, helper function collapses levels factor accordingly also ensures resulting levels order given group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"h_collapse_levels(x, group_list)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"x (factor) original factor. group_list (named list character) includes collapsing specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"transformed factor x new levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"set.seed(123) x <- factor(sample(   c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"MULTIPLE\", \"UNKNOWN\", \"WHITE\"),   size = 30L,   replace = TRUE )) group_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) x_collapsed <- h_collapse_levels(x, group_list) stopifnot(identical(levels(x_collapsed), names(group_list)))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Extract Words — h_extract_words","title":"Helper Function to Extract Words — h_extract_words","text":"helper function extracts words string. words defined containing lower upper case letters, colons dots. characters considered separators.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Extract Words — h_extract_words","text":"x (string) input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Extract Words — h_extract_words","text":"Character vector extracted words.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(\"a, b, , c, 234; 34562 - GeneID:bla\") #> [1] \"a\"          \"b\"          \"c\"          \"234\"        \"34562\"      #> [6] \"GeneID:bla\" h_extract_words(\"GeneID:1820, sdf.393; 32596\") #> [1] \"GeneID:1820\" \"sdf.393\"     \"32596\""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Format Gene Choices — h_gene_data","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Given hermes::AnyHermesData data object, well annotation column name use gene name, function formats contained genes data.frame ready consumption h_order_genes() e.g.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"h_gene_data(object, name_annotation)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Format Gene Choices — h_gene_data","text":"object (AnyHermesData) contains RNA-seq values one experiment. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Format Gene Choices — h_gene_data","text":"data.frame id name columns containing genes object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Note missing names names contain whitespace replaced empty strings consistency better labeling UI downstream","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"object <- hermes::hermes_data[1:10, ] h_gene_data(object, \"symbol\") #>                  id         name #> 1      GeneID:11185         INMT #> 2      GeneID:10677         AVIL #> 3  GeneID:101928428 LOC101928428 #> 4  GeneID:100422835      MIR3183 #> 5  GeneID:102466731     MIR6769A #> 6      GeneID:64881       PCDH20 #> 7     GeneID:286205         SCAI #> 8       GeneID:8365     HIST1H4H #> 9       GeneID:6804        STX1A #> 10 GeneID:100423018    MIR3156-3"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"function help merging MAE ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"h_km_mae_to_adtte(   adtte,   mae,   genes,   experiment_name = \"hd1\",   assay_name = \"counts\",   usubjid_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"adtte (data frame) adtte dataset. mae (MultiAssayExperiment) contains AnyHermesData objects. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups. usubjid_var (string) variable name subject ID variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"data frame containing columns/rows adtte match subject ID row names MAE gene samples available given experiment. attribute gene_cols contains column names gene columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"final gene column names can start different string original gene IDs (labels), particular white space colons removed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"library(dplyr) mae <- hermes::multi_assay_experiment adtte <- teal.modules.hermes::rADTTE %>%   dplyr::mutate(CNSR = as.logical(CNSR))  new_adtte <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(\"GeneID:1820\"),   experiment_name = \"hd2\" ) new_adtte2 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(\"GeneID:1820\", \"GeneID:94115\"), fun = colMeans),   experiment_name = \"hd2\" ) new_adtte3 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(A = \"GeneID:1820\", B = \"GeneID:94115\")),   experiment_name = \"hd2\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Order Gene Choices — h_order_genes","title":"Helper Function to Order Gene Choices — h_order_genes","text":"possible gene choices ordered follows. First come genes non-empty name, ordered name alphabetically. Last come genes empty name, ordered ID alphabetically.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"h_order_genes(genes)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Order Gene Choices — h_order_genes","text":"genes (data.frame) containing id name columns gene choices. Note missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Order Gene Choices — h_order_genes","text":"ordered data.frame.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"genes <- data.frame(   id = c(\"7\", \"1\", \"2\", \"345346\", \"0\"),   name = c(\"e\", \"\", \"c\", \"\", \"a\") ) h_order_genes(genes) #>       id name #> 5      0    a #> 3      2    c #> 1      7    e #> 2      1      #> 4 345346"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Parse Genes — h_parse_genes","title":"Helper Function to Parse Genes — h_parse_genes","text":"helper function takes vector words tries match id name columns possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(words, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Parse Genes — h_parse_genes","text":"words (character) containing gene IDs names. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Parse Genes — h_parse_genes","text":"subset choices matches words ID name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(   c(\"a\", \"2535\"),   data.frame(id = as.character(2533:2537), name = letters[1:5]) ) #>     id name #> 1 2533    a #> 3 2535    c"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Update Gene Selection — h_update_gene_selection","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"helper function takes intersection selected choices genes updates inputId accordingly. shows notification selected genes available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"","code":"h_update_gene_selection(session, inputId, selected, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"session (ShinySession) session object. inputId (string) ID used call module input. selected (character) currently selected gene IDs. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Heatmap Plot — heatmap_plot","title":"Correlation Heatmap Plot — heatmap_plot","text":"function plots correlation heatmap.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"heatmap_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Heatmap Plot — heatmap_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation Heatmap Plot — heatmap_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"library(hermes) #> Loading required package: ggfortify #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #>  #> Attaching package: ‘matrixStats’ #> The following object is masked from ‘package:dplyr’: #>  #>     count #>  #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #>  #>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #>     colWeightedMeans, colWeightedMedians, colWeightedSds, #>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #>     rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #>  #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:dplyr’: #>  #>     combine, intersect, setdiff, union #> The following objects are masked from ‘package:stats’: #>  #>     IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #>  #>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #>     as.data.frame, basename, cbind, colnames, dirname, do.call, #>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, #>     union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #>  #> Attaching package: ‘S4Vectors’ #> The following objects are masked from ‘package:dplyr’: #>  #>     first, rename #> The following object is masked from ‘package:utils’: #>  #>     findMatches #> The following objects are masked from ‘package:base’: #>  #>     I, expand.grid, unname #> Loading required package: IRanges #>  #> Attaching package: ‘IRanges’ #> The following objects are masked from ‘package:dplyr’: #>  #>     collapse, desc, slice #> Loading required package: GenomeInfoDb #> Loading required package: Biobase #> Welcome to Bioconductor #>  #>     Vignettes contain introductory material; view with #>     'browseVignettes()'. To cite Bioconductor, see #>     'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #>  #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #>  #>     rowMedians #> The following objects are masked from ‘package:matrixStats’: #>  #>     anyMissing, rowMedians #>  #> Attaching package: ‘hermes’ #> The following object is masked from ‘package:dplyr’: #>  #>     filter #> The following object is masked from ‘package:stats’: #>  #>     filter object <- HermesData(summarized_experiment) result <- heatmap_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty String — is_blank","title":"Checking for Empty String — is_blank","text":"predicate function helpful functions arguments yet initialized teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty String — is_blank","text":"x object check.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty String — is_blank","text":"Flag whether x identical empty string, .e. \"\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(\"\") #> [1] TRUE is_blank(\" \") #> [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists conventional arguments hermes teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. label (string) menu item label module teal app. inputId (string) ID used call module input. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . reporter (Reporter) object pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. .test (flag) whether display internal structure plot testing purposes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"multiple sample variables used given module, wrapper makes much easier specify server function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"multiSampleVarSpecServer(inputIds, original_data, ...)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"inputIds (character) multiple input IDs corresponding different sample variables specified UI function. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. ... additional arguments documented sampleVarSpecServer(), namely mandatory experiment_name optional categorical_only, num_levels label_modal_title. transformed_data assign_lists specified already specified internally .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"List final transformed experiment_data reactive list vars contains selected sample variables reactives input ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"if (FALSE) { # \\dontrun{ # In the server use: sample_var_specs <- multiSampleVarSpecServer(   inputIds = c(\"facet_var\", \"color_var\"),   experiment_name = reactive({     input$experiment_name   }),   original_data = ori_data # nolint Please update the <ori_data> ) # Then can extract the transformed data and selected variables later: experiment_data <- sample_var_specs$experiment_data() facet_var <- sample_var_specs$vars$facet_var() color_var <- sample_var_specs$vars$color_var() } # }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Sample Variable Specification — sampleVarSpecInput","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"defines input sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(   inputId,   label_vars = \"Select sample variable\",   label_levels_button = \"Combine factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"inputId (string) ID used call module input. label_vars (string) label sample variable selection. label_levels_button (string) label levels combination button.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(\"my_vars\", label_vars = \"Select faceting variable\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select faceting variable<\/label> #>   <\/div> #>   <div class=\"col-sm-4\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_vars-levels_button\" title=\"Combine factor levels\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-table\" role=\"presentation\" aria-label=\"table icon\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div> #>     <script> #>         $(function() { #>           $('#my_vars-sample_var').on('change', function(e) { #>             var select_concat = $(this).val().length ? $(this).val().join(', ') : 'NULL'; #>             $('#my_vars-sample_var_selected_text').html(select_concat); #>           }) #>         })<\/script> #>     <div> #>       <div id=\"my_vars-sample_var_input\" style=\"display: block;\"> #>         <div class=\"form-group shiny-input-container\"> #>           <label class=\"control-label shiny-label-null\" for=\"my_vars-sample_var\" id=\"my_vars-sample_var-label\"><\/label> #>           <select data-actions-box=\"false\" data-none-selected-text=\"- Nothing selected -\" data-max-options=\"1\" data-show-subtext=\"true\" data-live-search=\"false\" data-state-input=\"true\" id=\"my_vars-sample_var\" class=\"selectpicker form-control\" autocomplete=\"off\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>         <\/div> #>       <\/div> #>       <div id=\"my_vars-sample_var_fixed\" style=\"display: none;\"> #>         <label class=\"control-label\"><\/label> #>         <code id=\"my_vars-sample_var_selected_text\">NULL<\/code> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Sample Variable Specification — sampleVarSpecServer","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"defines server part sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"sampleVarSpecServer(   id,   experiment_name,   original_data,   transformed_data = original_data,   assign_lists = reactiveValues(),   num_levels = NULL,   categorical_only = !is.null(num_levels),   explicit_na = FALSE,   label_modal_title = \"Please click to group the original factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"id (string) shiny module id. experiment_name (reactive string) name input experiment. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. transformed_data (reactive SummarizedExperiment) used multiple sample variables can selected app. case, pass pre-transformed data. assign_lists (reactivevalues) object share factor level groupings across multiple sample variables. num_levels (count NULL) required number levels combining original levels. NULL numbers levels allowed. categorical_only (flag) whether categorical variables selected . explicit_na (flag) whether colData original_data transformed hermes::h_df_factors_with_explicit_na processing. means also NA made explicit factor level counted num_levels. label_modal_title (string) title dialog asks text input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"Reactive SummarizedExperiment::SummarizedExperiment can used input relevant hermes functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"atomic columns (e.g. DataFrame columns) colData completely missing (NA) shown selection. num_levels specified factor columns available.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"ui <- function(id) {   checkmate::assert_class(data, \"teal_data\")   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = plotOutput(ns(\"plot\"))   ) } server <- function(id,                    data) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       mae <- data()[[\"MAE\"]]       experiment_name_choices <- names(mae)       tags$div(         selectInput(session$ns(\"experiment_name\"), \"Select experiment\", experiment_name_choices),         sampleVarSpecInput(session$ns(\"facet_var\"), \"Select faceting variable\")       )     })     experiment_data <- reactive({       req(input$experiment_name)       mae <- data()[[\"MAE\"]]       object <- mae[[input$experiment_name]]       SummarizedExperiment::colData(object) <-         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))       object     })     facet_var_spec <- sampleVarSpecServer(       \"facet_var\",       experiment_name = reactive({         input$experiment_name       }),       original_data = experiment_data     )     output$plot <- renderPlot({       experiment_data_final <- facet_var_spec$experiment_data()       facet_var <- facet_var_spec$sample_var()       hermes::draw_boxplot(         experiment_data_final,         assay_name = \"counts\",         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),         facet_var = facet_var       )     })   }) } my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"sampleVarSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/teal.modules.hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.modules.hermes Package — teal.modules.hermes-package","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"teal.modules.hermes provides RNA-seq analysis modules add teal application.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/teal.modules.hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"Maintainer: Dony Unardi unardid@gene.com Authors: Daniel Sabanés Bové Nikolas Burkoff Dinakar Kulkarni Konrad Pagacz Namrata Bhatia Dawid Kaledkowski Pawel Rucki Jeff Luong Stefanie Bienert Haocheng Li Lyndsee Midori Zhang contributors: Sorin Voicu [contributor] Benoit Falquet [contributor] Mahmoud Hallal [contributor] Tim Treis [contributor] Vedha Viyash [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Barplot — tm_g_barplot","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"module provides interactive barplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"tm_g_barplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_barplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_barplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_barplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"ui_g_barplot(): sets user interface. srv_g_barplot(): sets server reactive graph. sample_tm_g_barplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_barplot(       label = \"barplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_barplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_barplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"module provides interactive boxplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"tm_g_boxplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(None = NULL, Mean = colMeans, Median = matrixStats::colMedians, Max     = matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_boxplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_boxplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_boxplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"ui_g_boxplot(): sets user interface. srv_g_boxplot(): sets server reactive graph. sample_tm_g_boxplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_boxplot(       label = \"boxplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_boxplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_boxplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Survival Forest Plot — tm_g_forest_tte","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"module provides interactive survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = c(1360L, 500L, 2000L),   .test = FALSE )  ui_g_forest_tte(   id,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_forest_tte(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   exclude_assays,   summary_funs,   plot_height,   plot_width,   .test = FALSE )  sample_tm_g_forest_tte(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"ui_g_forest_tte(): sets user interface. srv_g_forest_tte(): sets server reactive graph. sample_tm_g_forest_tte(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")  app <- init(   data = data,   modules = modules(     tm_g_forest_tte(       label = \"forestplot\",       adtte_name = \"ADTTE\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_forest_tte #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_forest_tte() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Kaplan-Meier Plot — tm_g_km","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"teal module produces grid style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_km(   id,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_km(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   summary_funs,   exclude_assays,   .test = FALSE )  sample_tm_g_km(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"ui_g_km(): sets user interface. srv_g_km(): sets user interface. sample_tm_g_km(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")   modules <- modules(   tm_g_km(     label = \"kaplan-meier\",     adtte_name = \"ADTTE\",     mae_name = \"MAE\"   ) ) #> Initializing tm_g_km  app <- init(   data = data,   modules = modules ) #> Initializing reporter_previewer_module  if (interactive()) {   shinyApp(ui = app$ui, server = app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_km() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for PCA Analysis — tm_g_pca","title":"Teal Module for PCA Analysis — tm_g_pca","text":"module provides interactive principal components plot interactive heatmap correlation principal components sample variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"tm_g_pca(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_pca(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_pca(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_pca(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for PCA Analysis — tm_g_pca","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for PCA Analysis — tm_g_pca","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for PCA Analysis — tm_g_pca","text":"ui_g_pca(): sets user interface. srv_g_pca(): sets server reactive graph. sample_tm_g_pca(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_pca(       label = \"PCA plot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_pca #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_pca() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Quality Control — tm_g_quality","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"module adds quality flags, filters genes /samples, normalizes AnyHermesData objects provides interactive plots RNA-seq gene expression quality control.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"tm_g_quality(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_quality(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_quality(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_quality(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"ui_g_quality(): sets user interface. srv_g_quality(): sets server reactive graphs. sample_tm_g_quality(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_quality(       label = \"Quality Control\",       mae_name = \"MAE\"     )   ) ) #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_quality() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"module provides interactive scatterplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"tm_g_scatterplot(   label,   mae_name,   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_scatterplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_scatterplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_scatterplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"ui_g_scatterplot(): sets user interface. srv_g_scatterplot(): sets server reactive graph. sample_tm_g_scatterplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_scatterplot(       label = \"scatterplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_scatterplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_scatterplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"module provides interactive volcano plot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"tm_g_volcanoplot(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_volcanoplot(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_volcanoplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_volcanoplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"ui_g_volcanoplot(): sets user interface. srv_g_volcanoplot(): sets server reactive graph. sample_tm_g_volcanoplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_volcanoplot(       label = \"volcanoplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_volcanoplot #> Initializing reporter_previewer_module if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_volcanoplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Most Expressed Genes Plot — top_gene_plot","title":"Most Expressed Genes Plot — top_gene_plot","text":"function plots expressed genes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"top_gene_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Most Expressed Genes Plot — top_gene_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Most Expressed Genes Plot — top_gene_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"library(hermes) object <- HermesData(summarized_experiment) result <- top_gene_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Gene Specification — validate_gene_spec","title":"Validation of Gene Specification — validate_gene_spec","text":"validation function checks given hermes::GeneSpec least one gene selected genes included possible choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Gene Specification — validate_gene_spec","text":"","code":"validate_gene_spec(gene_spec, gene_choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Gene Specification — validate_gene_spec","text":"gene_spec (GeneSpec) gene specification. gene_choices (character) possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Number of Levels — validate_n_levels","title":"Validation of Number of Levels — validate_n_levels","text":"validation function checks given vector x factor specified number levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Number of Levels — validate_n_levels","text":"","code":"validate_n_levels(x, name, n_levels)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Number of Levels — validate_n_levels","text":"x (factor) factor validate. name (string) name x app. n_levels (count) required number factor levels x.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-6-9023","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.6.9023","text":"Added placeholders assaySpec, adtteSpec geneSpec inputs option selected. Disabled select input assaySpec adtteSpec options available. module developers: module gets teal_data object UI reactive(<teal_data>) server","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"enhancements-0-1-6-9023","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.hermes 0.1.6.9023","text":"Updated documentation vignettes new way specifying data teal::init(). data argument accepts teal_data object. Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"bug-fixes-0-1-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.5","text":"Filtering data filter panel now correctly triggers sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"breaking-changes-0-1-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.hermes 0.1.5","text":"Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5","text":"Removed scda dependencies. Migrate shinytest2.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-014","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.4","title":"teal.modules.hermes 0.1.4","text":"Added teal.reporter functionality modules. Add installation instruction","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-013","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.3","title":"teal.modules.hermes 0.1.3","text":"Improve selection sample variables forest module (tm_g_forest_tte) categorical variables can selected first place.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.3","text":"Added template pkgdown site. Updated package authors. Added option categorical_only sampleVarSpec server module, allows show categorical sample variables selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-012","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.2","title":"teal.modules.hermes 0.1.2","text":"Rewrote modules use moduleServer updated call plot_with_settings_srv changes teal.devel. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Added basic logging modules. Fixed geneSpecInput hermes app doesn’t fail anymore (chrome) experiment genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.1","text":"Updated legend PCA plot. Gene selection thousand genes longer hangs application. achieved different selection input corresponding geneSpec shiny module. atomic columns colData least one value can now selected sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.1","text":"Updated R version requirement >= 3.6. Updated sampleVarSpec geneSpec modules new icons remove warnings using shiny version >= 1.7. Removed dependencies deprecated packages utils.nest test.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-010","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.0","title":"teal.modules.hermes 0.1.0","text":"First release teal.modules.hermes package, contains teal modules RNA-seq analysis using hermes package. New users first begin reading README.md teal.modules.hermes package become familiar.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.hermes 0.1.0","text":"tm_g_barplot barplot module RNA-seq gene expression analysis. tm_g_boxplot boxplot module RNA-seq gene expression analysis. tm_g_forest_tte survival forest plot module analyze RNA-seq gene expression data together survival data. tm_g_km Kaplan-Meier plot module analyze RNA-seq gene expression data together survival data. tm_g_pca principal components analysis plot module RNA-seq gene expression analysis. tm_g_quality quality control module RNA-seq gene expression data. tm_g_scatterplot scatterplot module RNA-seq gene expression analysis. tm_g_volcanoplot differential gene expression analysis module.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.hermes/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.hermes/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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/teal.modules.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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id, mae_name) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = plotOutput(ns(\"awesome_plot\"))   ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input,                 output,                 session,                 data,                 filter_panel_api,                 mae_name) {   output$encoding_ui <- renderUI({     tags$div(       experimentSpecInput(session$ns(\"experiment\"), data, mae_name),       assaySpecInput(session$ns(\"assay\"))     )   })   experiment <- experimentSpecServer(     \"experiment\",     data = data,     filter_panel_api = filter_panel_api,     mae_name = mae_name,     name_annotation = NULL # If you have a gene name column in your rowData, can specify here.   )   assay <- assaySpecServer(\"assay\", experiment$assays)   output$awesome_plot <- renderPlot({     data <- experiment$data()     assay <- assay()     req(assay %in% SummarizedExperiment::assayNames(data))     counts <- SummarizedExperiment::assay(data, assay)     df <- data.frame(gene = rownames(counts), counts = rowSums(counts))     df <- na.omit(df[order(df$counts, decreasing = TRUE), ])     df$gene <- factor(df$gene, levels = df$gene)     df <- df[1:10, ]     ggplot(df, aes(x = gene, y = counts)) +       geom_col() +       theme(axis.text.x = element_text(angle = 90))   }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") {   mae_name <- \"MAE\"   data <- teal_data(MAE = hermes::lapply(mae, hermes::HermesData))   app <- init(     data = data,     modules = teal::modules(       module(         label = label,         server = srv,         server_args = list(mae_name = mae_name),         ui = ui,         ui_args = list(mae_name = mae_name),         datanames = mae_name       )     )   )   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dony Unardi. Maintainer. Daniel Sabanés Bové. Author. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. Vedha Viyash. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2024). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.6.9024, https://github.com/insightsengineering/teal.modules.hermes/, https://insightsengineering.github.io/teal.modules.hermes/.","code":"@Manual{,   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},   year = {2024},   note = {R package version 0.1.6.9024,     https://github.com/insightsengineering/teal.modules.hermes/},   url = {https://insightsengineering.github.io/teal.modules.hermes/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes@*release\")  # beta versions # install.packages(\"pak\") pak::pkg_install(\"insightsengineering/teal.modules.hermes\")"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer(   id,   data,   mae_name,   adtte_name,   adtte_vars,   experiment_data,   experiment_name,   assay,   genes,   probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  ui <- function(id) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = verbatimTextOutput(ns(\"summary\"))   ) }  server <- function(id, data, filter_panel_api) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(session$ns(\"experiment\"), data, mae_name = \"MAE\"),         assaySpecInput(session$ns(\"assay\")),         geneSpecInput(session$ns(\"genes\"), funs = list(Mean = colMeans)),         adtteSpecInput(session$ns(\"adtte\"))       )     })     experiment <- experimentSpecServer(       \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       assays = experiment$assays     )     genes <- geneSpecServer(       \"genes\",       funs = list(Mean = colMeans),       gene_choices = experiment$genes     )     adtte <- adtteSpecServer(       \"adtte\",       data = data,       adtte_name = \"ADTTE\",       mae_name = \"MAE\",       adtte_vars = list(         aval = \"AVAL\",         avalu = \"AVALU\",         is_event = \"is_event\",         paramcd = \"PARAMCD\",         usubjid = \"USUBJID\"       ),       experiment_data = experiment$data,       experiment_name = experiment$name,       assay = assay,       genes = genes,       probs = reactive({         0.5       })     )     output$summary <- renderPrint({       binned_adtte_subset <- adtte$binned_adtte_subset()       summary(binned_adtte_subset)     })   }) }  my_app <- function() {   data <- teal_data()   data <- within(data, {     ADSL <- teal.data::rADSL     ADTTE <- teal.modules.hermes::rADTTE %>%       dplyr::mutate(is_event = .data$CNSR == 0)     MAE <- hermes::multi_assay_experiment   })   datanames <- c(\"ADSL\", \"ADTTE\", \"MAE\")   datanames(data) <- datanames   join_keys(data) <- default_cdisc_join_keys[datanames]    app <- init(     data = data,     modules = modules(       module(         label = \"adtteSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) }  if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = textOutput(ns(\"result\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, module = function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(session$ns(\"experiment\"), data, \"MAE\"),         assaySpecInput(           session$ns(\"assay\"),           label_assays = \"Please choose assay\"         )       )     })     experiment <- experimentSpecServer(       id = \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       experiment$assays,       exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\")     )     output$result <- renderPrint({       assay()     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"assaySpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.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/teal.modules.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/teal.modules.hermes/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — 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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x)  assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)  test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE)  assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)  test_tag(x, null.ok = FALSE)  expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","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":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput(   inputId,   data,   mae_name,   label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer(   id,   data,   filter_panel_api,   mae_name,   name_annotation = \"symbol\",   sample_vars_as_factors = TRUE,   with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id,                mae_name) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = tags$div(       verbatimTextOutput(ns(\"summary\")),       verbatimTextOutput(ns(\"head\"))     )   ) }  server <- function(id,                    data,                    filter_panel_api,                    mae_name) {   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       tags$div(         experimentSpecInput(           session$ns(\"my_experiment\"),           data,           mae_name,           label_experiments = \"Please choose experiment\"         ),         selectInput(           session$ns(\"property\"),           \"Please choose property\",           c(\"data\", \"name\", \"genes\", \"assays\")         )       )     })     experiment <- experimentSpecServer(       \"my_experiment\",       data,       filter_panel_api,       mae_name     )     result <- reactive({       req(input$property)       switch(input$property,         data = experiment$data(),         name = experiment$name(),         genes = experiment$genes(),         assays = experiment$assays()       )     })     output$summary <- renderPrint({       result <- result()       hermes::summary(result)     })     output$head <- renderPrint({       result <- result()       utils::head(result)     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"experimentSpec example\",         server = server,         server_args = list(mae_name = \"MAE\"),         ui = ui,         ui_args = list(mae_name = \"MAE\"),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(   inputId,   funs,   label_genes = \"Select Gene(s)\",   label_funs = \"Select Gene Summary\",   label_text_button = \"Enter list of genes\",   label_lock_button =     \"Lock gene selection (so that it does not get updated when filtering)\",   label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"),   label_select_none_button = \"Select None\",   max_options = 200L,   max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select Gene(s)<\/label> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_none_button\" title=\"Select None\" type=\"button\"> #>       <span> #>         <i aria-label=\"remove-circle icon\" class=\"glyphicon glyphicon-remove-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_all_button\" title=\"Select All Genes (first 200)\" type=\"button\"> #>       <span> #>         <i aria-label=\"ok-circle icon\" class=\"glyphicon glyphicon-ok-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-text_button\" title=\"Enter list of genes\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-font\" role=\"presentation\" aria-label=\"font icon\"><\/i> #>       <\/span> #>     <\/button> #>     <div class=\"pull-right\" title=\"Lock gene selection (so that it does not get updated when filtering)\"> #>       <div class=\"form-group shiny-input-container\"> #>         <div class=\"pretty p-toggle p-plain p-icon p-pulse\"> #>           <input id=\"my_genes-lock_button\" type=\"checkbox\"/> #>           <div class=\"state p-on\"> #>             <i aria-label=\"lock icon\" class=\"fas fa-lock icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>           <div class=\"state p-off\"> #>             <i aria-label=\"lock-open icon\" class=\"fas fa-lock-open icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>         <\/div> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label shiny-label-null\" for=\"my_genes-genes\" id=\"my_genes-genes-label\"><\/label> #>     <div> #>       <select class=\"shiny-input-select form-control\" id=\"my_genes-genes\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-genes\" data-eval=\"[&quot;render&quot;]\">{\"placeholder\":\"- Nothing selected -\",\"render\":\"{\\n          option: function(item, escape) {\\n              return '<div> <span style=\\\"font-size: inherit;\\\">' + item.label + '<\\/div>' +\\n                ' <span style=\\\"color: #808080; font-size: xx-small;\\\" >' + item.value + '<\\/div> <\\/div>'\\n            }\\n          }\",\"searchField\":[\"value\",\"label\"],\"maxOptions\":200,\"maxItems\":200,\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"shiny-panel-conditional\" data-display-if=\"input.genes &amp;&amp; input.genes.length &gt; 1\" data-ns-prefix=\"my_genes-\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label\" id=\"my_genes-fun_name-label\" for=\"my_genes-fun_name\">Please select function<\/label> #>     <div> #>       <select id=\"my_genes-fun_name\" class=\"shiny-input-select\"><option value=\"mean\" selected>mean<\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-fun_name\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Gene Signature Specification — geneSpecServer","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"defines server part gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"geneSpecServer(   id,   funs,   gene_choices,   label_modal_title = \"Enter list of genes\",   label_modal_footer = c(\"Please enter a comma-separated list of gene IDs and/or names.\",     \"(Note that genes not included in current choices will be removed)\") )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"id (string) shiny module id. funs (static named list) names list used function selection drop menu. gene_choices (reactive data.frame) returns possible gene choices populate UI, data.frame columns id name. label_modal_title (string) title dialog asks text input. label_modal_footer (character) lines text use footer dialog.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"Reactive hermes::GeneSpec can used input relevant hermes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"ui <- function(id, funs) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = tags$div(       geneSpecInput(         ns(\"my_genes\"),         funs = funs,         label_funs = \"Please select function\"       )     ),     output = textOutput(ns(\"result\"))   ) } server <- function(id,                    data,                    funs) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     gene_choices <- reactive({       mae <- data()[[\"MAE\"]]       object <- mae[[1]]       gene_ids <- rownames(object)       gene_names <- SummarizedExperiment::rowData(object)$symbol       gene_data <- data.frame(         id = gene_ids,         name = gene_names       )       gene_data[order(gene_data$name), ]     })     gene_spec <- geneSpecServer(       \"my_genes\",       funs = funs,       gene_choices = gene_choices     )     output$result <- renderText({       validate_gene_spec(         gene_spec(),         gene_choices()$id       )       gene_spec <- gene_spec()       gene_spec$get_label()     })   }) } funs <- list(mean = colMeans) my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"GeneSpec example\",         server = server,         server_args = list(funs = funs),         ui = ui,         ui_args = list(funs = funs),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Group List Creation — h_assign_to_group_list","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"helper function takes assignment list converts group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"h_assign_to_group_list(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"x (named list character) input assignment list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"combination list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"assign_list <- list(   \"ASIAN\" = \"1\",   \"BLACK OR AFRICAN AMERICAN\" = \"1\",   \"MULTIPLE\" = \"2\",   \"UNKNOWN\" = \"2\",   \"WHITE\" = \"4\" ) objective_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) result_list <- h_assign_to_group_list(assign_list) stopifnot(identical(result_list, objective_list))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"Given group list factor, helper function collapses levels factor accordingly also ensures resulting levels order given group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"h_collapse_levels(x, group_list)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"x (factor) original factor. group_list (named list character) includes collapsing specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"transformed factor x new levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"set.seed(123) x <- factor(sample(   c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"MULTIPLE\", \"UNKNOWN\", \"WHITE\"),   size = 30L,   replace = TRUE )) group_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) x_collapsed <- h_collapse_levels(x, group_list) stopifnot(identical(levels(x_collapsed), names(group_list)))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Extract Words — h_extract_words","title":"Helper Function to Extract Words — h_extract_words","text":"helper function extracts words string. words defined containing lower upper case letters, colons dots. characters considered separators.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Extract Words — h_extract_words","text":"x (string) input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Extract Words — h_extract_words","text":"Character vector extracted words.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(\"a, b, , c, 234; 34562 - GeneID:bla\") #> [1] \"a\"          \"b\"          \"c\"          \"234\"        \"34562\"      #> [6] \"GeneID:bla\" h_extract_words(\"GeneID:1820, sdf.393; 32596\") #> [1] \"GeneID:1820\" \"sdf.393\"     \"32596\""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Format Gene Choices — h_gene_data","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Given hermes::AnyHermesData data object, well annotation column name use gene name, function formats contained genes data.frame ready consumption h_order_genes() e.g.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"h_gene_data(object, name_annotation)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Format Gene Choices — h_gene_data","text":"object (AnyHermesData) contains RNA-seq values one experiment. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Format Gene Choices — h_gene_data","text":"data.frame id name columns containing genes object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Note missing names names contain whitespace replaced empty strings consistency better labeling UI downstream","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"object <- hermes::hermes_data[1:10, ] h_gene_data(object, \"symbol\") #>                  id         name #> 1      GeneID:11185         INMT #> 2      GeneID:10677         AVIL #> 3  GeneID:101928428 LOC101928428 #> 4  GeneID:100422835      MIR3183 #> 5  GeneID:102466731     MIR6769A #> 6      GeneID:64881       PCDH20 #> 7     GeneID:286205         SCAI #> 8       GeneID:8365     HIST1H4H #> 9       GeneID:6804        STX1A #> 10 GeneID:100423018    MIR3156-3"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"function help merging MAE ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"h_km_mae_to_adtte(   adtte,   mae,   genes,   experiment_name = \"hd1\",   assay_name = \"counts\",   usubjid_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"adtte (data frame) adtte dataset. mae (MultiAssayExperiment) contains AnyHermesData objects. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups. usubjid_var (string) variable name subject ID variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"data frame containing columns/rows adtte match subject ID row names MAE gene samples available given experiment. attribute gene_cols contains column names gene columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"final gene column names can start different string original gene IDs (labels), particular white space colons removed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"library(dplyr) mae <- hermes::multi_assay_experiment adtte <- teal.modules.hermes::rADTTE %>%   dplyr::mutate(CNSR = as.logical(CNSR))  new_adtte <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(\"GeneID:1820\"),   experiment_name = \"hd2\" ) new_adtte2 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(\"GeneID:1820\", \"GeneID:94115\"), fun = colMeans),   experiment_name = \"hd2\" ) new_adtte3 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(A = \"GeneID:1820\", B = \"GeneID:94115\")),   experiment_name = \"hd2\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Order Gene Choices — h_order_genes","title":"Helper Function to Order Gene Choices — h_order_genes","text":"possible gene choices ordered follows. First come genes non-empty name, ordered name alphabetically. Last come genes empty name, ordered ID alphabetically.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"h_order_genes(genes)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Order Gene Choices — h_order_genes","text":"genes (data.frame) containing id name columns gene choices. Note missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Order Gene Choices — h_order_genes","text":"ordered data.frame.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"genes <- data.frame(   id = c(\"7\", \"1\", \"2\", \"345346\", \"0\"),   name = c(\"e\", \"\", \"c\", \"\", \"a\") ) h_order_genes(genes) #>       id name #> 5      0    a #> 3      2    c #> 1      7    e #> 2      1      #> 4 345346"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Parse Genes — h_parse_genes","title":"Helper Function to Parse Genes — h_parse_genes","text":"helper function takes vector words tries match id name columns possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(words, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Parse Genes — h_parse_genes","text":"words (character) containing gene IDs names. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Parse Genes — h_parse_genes","text":"subset choices matches words ID name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(   c(\"a\", \"2535\"),   data.frame(id = as.character(2533:2537), name = letters[1:5]) ) #>     id name #> 1 2533    a #> 3 2535    c"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Update Gene Selection — h_update_gene_selection","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"helper function takes intersection selected choices genes updates inputId accordingly. shows notification selected genes available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"","code":"h_update_gene_selection(session, inputId, selected, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"session (ShinySession) session object. inputId (string) ID used call module input. selected (character) currently selected gene IDs. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Heatmap Plot — heatmap_plot","title":"Correlation Heatmap Plot — heatmap_plot","text":"function plots correlation heatmap.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"heatmap_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Heatmap Plot — heatmap_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation Heatmap Plot — heatmap_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"library(hermes) #> Loading required package: ggfortify #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #>  #> Attaching package: ‘matrixStats’ #> The following object is masked from ‘package:dplyr’: #>  #>     count #>  #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #>  #>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #>     colWeightedMeans, colWeightedMedians, colWeightedSds, #>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #>     rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #>  #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:dplyr’: #>  #>     combine, intersect, setdiff, union #> The following objects are masked from ‘package:stats’: #>  #>     IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #>  #>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #>     as.data.frame, basename, cbind, colnames, dirname, do.call, #>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, #>     tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #>  #> Attaching package: ‘S4Vectors’ #> The following objects are masked from ‘package:dplyr’: #>  #>     first, rename #> The following object is masked from ‘package:utils’: #>  #>     findMatches #> The following objects are masked from ‘package:base’: #>  #>     I, expand.grid, unname #> Loading required package: IRanges #>  #> Attaching package: ‘IRanges’ #> The following objects are masked from ‘package:dplyr’: #>  #>     collapse, desc, slice #> Loading required package: GenomeInfoDb #> Loading required package: Biobase #> Welcome to Bioconductor #>  #>     Vignettes contain introductory material; view with #>     'browseVignettes()'. To cite Bioconductor, see #>     'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #>  #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #>  #>     rowMedians #> The following objects are masked from ‘package:matrixStats’: #>  #>     anyMissing, rowMedians #>  #> Attaching package: ‘hermes’ #> The following object is masked from ‘package:dplyr’: #>  #>     filter #> The following object is masked from ‘package:stats’: #>  #>     filter object <- HermesData(summarized_experiment) result <- heatmap_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty String — is_blank","title":"Checking for Empty String — is_blank","text":"predicate function helpful functions arguments yet initialized teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty String — is_blank","text":"x object check.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty String — is_blank","text":"Flag whether x identical empty string, .e. \"\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(\"\") #> [1] TRUE is_blank(\" \") #> [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists conventional arguments hermes teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. label (string) menu item label module teal app. inputId (string) ID used call module input. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . reporter (Reporter) object pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. .test (flag) whether display internal structure plot testing purposes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"multiple sample variables used given module, wrapper makes much easier specify server function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"multiSampleVarSpecServer(inputIds, original_data, ...)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"inputIds (character) multiple input IDs corresponding different sample variables specified UI function. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. ... additional arguments documented sampleVarSpecServer(), namely mandatory experiment_name optional categorical_only, num_levels label_modal_title. transformed_data assign_lists specified already specified internally .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"List final transformed experiment_data reactive list vars contains selected sample variables reactives input ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"if (FALSE) { # \\dontrun{ # In the server use: sample_var_specs <- multiSampleVarSpecServer(   inputIds = c(\"facet_var\", \"color_var\"),   experiment_name = reactive({     input$experiment_name   }),   original_data = ori_data # nolint Please update the <ori_data> ) # Then can extract the transformed data and selected variables later: experiment_data <- sample_var_specs$experiment_data() facet_var <- sample_var_specs$vars$facet_var() color_var <- sample_var_specs$vars$color_var() } # }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Sample Variable Specification — sampleVarSpecInput","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"defines input sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(   inputId,   label_vars = \"Select sample variable\",   label_levels_button = \"Combine factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"inputId (string) ID used call module input. label_vars (string) label sample variable selection. label_levels_button (string) label levels combination button.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(\"my_vars\", label_vars = \"Select faceting variable\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select faceting variable<\/label> #>   <\/div> #>   <div class=\"col-sm-4\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_vars-levels_button\" title=\"Combine factor levels\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-table\" role=\"presentation\" aria-label=\"table icon\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div> #>     <script> #>         $(function() { #>           $('#my_vars-sample_var').on('change', function(e) { #>             var select_concat = $(this).val().length ? $(this).val().join(', ') : 'NULL'; #>             $('#my_vars-sample_var_selected_text').html(select_concat); #>           }) #>         })<\/script> #>     <div> #>       <div id=\"my_vars-sample_var_input\" style=\"display: block;\"> #>         <div class=\"form-group shiny-input-container\"> #>           <label class=\"control-label shiny-label-null\" for=\"my_vars-sample_var\" id=\"my_vars-sample_var-label\"><\/label> #>           <select data-actions-box=\"false\" data-none-selected-text=\"- Nothing selected -\" data-max-options=\"1\" data-show-subtext=\"true\" data-live-search=\"false\" data-state-input=\"true\" id=\"my_vars-sample_var\" class=\"selectpicker form-control\" autocomplete=\"off\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>         <\/div> #>       <\/div> #>       <div id=\"my_vars-sample_var_fixed\" style=\"display: none;\"> #>         <label class=\"control-label\"><\/label> #>         <code id=\"my_vars-sample_var_selected_text\">NULL<\/code> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Sample Variable Specification — sampleVarSpecServer","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"defines server part sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"sampleVarSpecServer(   id,   experiment_name,   original_data,   transformed_data = original_data,   assign_lists = reactiveValues(),   num_levels = NULL,   categorical_only = !is.null(num_levels),   explicit_na = FALSE,   label_modal_title = \"Please click to group the original factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"id (string) shiny module id. experiment_name (reactive string) name input experiment. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. transformed_data (reactive SummarizedExperiment) used multiple sample variables can selected app. case, pass pre-transformed data. assign_lists (reactivevalues) object share factor level groupings across multiple sample variables. num_levels (count NULL) required number levels combining original levels. NULL numbers levels allowed. categorical_only (flag) whether categorical variables selected . explicit_na (flag) whether colData original_data transformed hermes::h_df_factors_with_explicit_na processing. means also NA made explicit factor level counted num_levels. label_modal_title (string) title dialog asks text input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"Reactive SummarizedExperiment::SummarizedExperiment can used input relevant hermes functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"atomic columns (e.g. DataFrame columns) colData completely missing (NA) shown selection. num_levels specified factor columns available.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"ui <- function(id) {   checkmate::assert_class(data, \"teal_data\")   ns <- NS(id)    teal.widgets::standard_layout(     encoding = uiOutput(ns(\"encoding_ui\")),     output = plotOutput(ns(\"plot\"))   ) } server <- function(id,                    data) {   checkmate::assert_class(data, \"reactive\")   checkmate::assert_class(shiny::isolate(data()), \"teal_data\")   moduleServer(id, function(input, output, session) {     output$encoding_ui <- renderUI({       mae <- data()[[\"MAE\"]]       experiment_name_choices <- names(mae)       tags$div(         selectInput(session$ns(\"experiment_name\"), \"Select experiment\", experiment_name_choices),         sampleVarSpecInput(session$ns(\"facet_var\"), \"Select faceting variable\")       )     })     experiment_data <- reactive({       req(input$experiment_name)       mae <- data()[[\"MAE\"]]       object <- mae[[input$experiment_name]]       SummarizedExperiment::colData(object) <-         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))       object     })     facet_var_spec <- sampleVarSpecServer(       \"facet_var\",       experiment_name = reactive({         input$experiment_name       }),       original_data = experiment_data     )     output$plot <- renderPlot({       experiment_data_final <- facet_var_spec$experiment_data()       facet_var <- facet_var_spec$sample_var()       hermes::draw_boxplot(         experiment_data_final,         assay_name = \"counts\",         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),         facet_var = facet_var       )     })   }) } my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"sampleVarSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/teal.modules.hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.modules.hermes Package — teal.modules.hermes-package","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"teal.modules.hermes provides RNA-seq analysis modules add teal application.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/teal.modules.hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"Maintainer: Dony Unardi unardid@gene.com Authors: Daniel Sabanés Bové Nikolas Burkoff Dinakar Kulkarni Konrad Pagacz Namrata Bhatia Dawid Kaledkowski Pawel Rucki Jeff Luong Stefanie Bienert Haocheng Li Lyndsee Midori Zhang contributors: Sorin Voicu [contributor] Benoit Falquet [contributor] Mahmoud Hallal [contributor] Tim Treis [contributor] Vedha Viyash [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Barplot — tm_g_barplot","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"module provides interactive barplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"tm_g_barplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_barplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_barplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_barplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"ui_g_barplot(): sets user interface. srv_g_barplot(): sets server reactive graph. sample_tm_g_barplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_barplot(       label = \"barplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_barplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_barplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"module provides interactive boxplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"tm_g_boxplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(None = NULL, Mean = colMeans, Median = matrixStats::colMedians, Max     = matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_boxplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_boxplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_boxplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"ui_g_boxplot(): sets user interface. srv_g_boxplot(): sets server reactive graph. sample_tm_g_boxplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_boxplot(       label = \"boxplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_boxplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_boxplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Survival Forest Plot — tm_g_forest_tte","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"module provides interactive survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = c(1360L, 500L, 2000L),   .test = FALSE )  ui_g_forest_tte(   id,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_forest_tte(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   exclude_assays,   summary_funs,   plot_height,   plot_width,   .test = FALSE )  sample_tm_g_forest_tte(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"ui_g_forest_tte(): sets user interface. srv_g_forest_tte(): sets server reactive graph. sample_tm_g_forest_tte(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")  app <- init(   data = data,   modules = modules(     tm_g_forest_tte(       label = \"forestplot\",       adtte_name = \"ADTTE\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_forest_tte if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_forest_tte() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Kaplan-Meier Plot — tm_g_km","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"teal module produces grid style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_km(   id,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_km(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   summary_funs,   exclude_assays,   .test = FALSE )  sample_tm_g_km(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"ui_g_km(): sets user interface. srv_g_km(): sets user interface. sample_tm_g_km(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"library(dplyr)  data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")   modules <- modules(   tm_g_km(     label = \"kaplan-meier\",     adtte_name = \"ADTTE\",     mae_name = \"MAE\"   ) ) #> Initializing tm_g_km  app <- init(   data = data,   modules = modules )  if (interactive()) {   shinyApp(ui = app$ui, server = app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_km() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for PCA Analysis — tm_g_pca","title":"Teal Module for PCA Analysis — tm_g_pca","text":"module provides interactive principal components plot interactive heatmap correlation principal components sample variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"tm_g_pca(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_pca(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_pca(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_pca(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for PCA Analysis — tm_g_pca","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for PCA Analysis — tm_g_pca","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for PCA Analysis — tm_g_pca","text":"ui_g_pca(): sets user interface. srv_g_pca(): sets server reactive graph. sample_tm_g_pca(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_pca(       label = \"PCA plot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_pca if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_pca() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Quality Control — tm_g_quality","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"module adds quality flags, filters genes /samples, normalizes AnyHermesData objects provides interactive plots RNA-seq gene expression quality control.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"tm_g_quality(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_quality(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_quality(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_quality(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"ui_g_quality(): sets user interface. srv_g_quality(): sets server reactive graphs. sample_tm_g_quality(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_quality(       label = \"Quality Control\",       mae_name = \"MAE\"     )   ) ) if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_quality() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"module provides interactive scatterplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"tm_g_scatterplot(   label,   mae_name,   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_scatterplot(   id,   mae_name,   summary_funs,   pre_output,   post_output,   .test = FALSE )  srv_g_scatterplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs,   .test = FALSE )  sample_tm_g_scatterplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"ui_g_scatterplot(): sets user interface. srv_g_scatterplot(): sets server reactive graph. sample_tm_g_scatterplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_scatterplot(       label = \"scatterplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_scatterplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_scatterplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"module provides interactive volcano plot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"tm_g_volcanoplot(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL,   .test = FALSE )  ui_g_volcanoplot(id, mae_name, pre_output, post_output, .test = FALSE)  srv_g_volcanoplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   .test = FALSE )  sample_tm_g_volcanoplot(.test = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). .test (flag) whether display internal structure plot testing purposes. id (string) shiny module id. data (reactive)reactive(<teal_data>) holding data sets provided app initialization going filters. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"ui_g_volcanoplot(): sets user interface. srv_g_volcanoplot(): sets server reactive graph. sample_tm_g_volcanoplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_volcanoplot(       label = \"volcanoplot\",       mae_name = \"MAE\"     )   ) ) #> Initializing tm_g_volcanoplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_volcanoplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Most Expressed Genes Plot — top_gene_plot","title":"Most Expressed Genes Plot — top_gene_plot","text":"function plots expressed genes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"top_gene_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Most Expressed Genes Plot — top_gene_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Most Expressed Genes Plot — top_gene_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"library(hermes) object <- HermesData(summarized_experiment) result <- top_gene_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Gene Specification — validate_gene_spec","title":"Validation of Gene Specification — validate_gene_spec","text":"validation function checks given hermes::GeneSpec least one gene selected genes included possible choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Gene Specification — validate_gene_spec","text":"","code":"validate_gene_spec(gene_spec, gene_choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Gene Specification — validate_gene_spec","text":"gene_spec (GeneSpec) gene specification. gene_choices (character) possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Number of Levels — validate_n_levels","title":"Validation of Number of Levels — validate_n_levels","text":"validation function checks given vector x factor specified number levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Number of Levels — validate_n_levels","text":"","code":"validate_n_levels(x, name, n_levels)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Number of Levels — validate_n_levels","text":"x (factor) factor validate. name (string) name x app. n_levels (count) required number factor levels x.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-6-9024","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.6.9024","text":"Added placeholders assaySpec, adtteSpec geneSpec inputs option selected. Disabled select input assaySpec adtteSpec options available. module developers: module gets teal_data object UI reactive(<teal_data>) server","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"enhancements-0-1-6-9024","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.hermes 0.1.6.9024","text":"Updated documentation vignettes new way specifying data teal::init(). data argument accepts teal_data object. Added teal.logger functionality logging changes shiny inputs modules.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"bug-fixes-0-1-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.5","text":"Filtering data filter panel now correctly triggers sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"breaking-changes-0-1-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.hermes 0.1.5","text":"Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5","text":"Removed scda dependencies. Migrate shinytest2.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-014","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.4","title":"teal.modules.hermes 0.1.4","text":"Added teal.reporter functionality modules. Add installation instruction","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-013","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.3","title":"teal.modules.hermes 0.1.3","text":"Improve selection sample variables forest module (tm_g_forest_tte) categorical variables can selected first place.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.3","text":"Added template pkgdown site. Updated package authors. Added option categorical_only sampleVarSpec server module, allows show categorical sample variables selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-012","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.2","title":"teal.modules.hermes 0.1.2","text":"Rewrote modules use moduleServer updated call plot_with_settings_srv changes teal.devel. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Added basic logging modules. Fixed geneSpecInput hermes app doesn’t fail anymore (chrome) experiment genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.1","text":"Updated legend PCA plot. Gene selection thousand genes longer hangs application. achieved different selection input corresponding geneSpec shiny module. atomic columns colData least one value can now selected sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.1","text":"Updated R version requirement >= 3.6. Updated sampleVarSpec geneSpec modules new icons remove warnings using shiny version >= 1.7. Removed dependencies deprecated packages utils.nest test.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-010","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.0","title":"teal.modules.hermes 0.1.0","text":"First release teal.modules.hermes package, contains teal modules RNA-seq analysis using hermes package. New users first begin reading README.md teal.modules.hermes package become familiar.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.hermes 0.1.0","text":"tm_g_barplot barplot module RNA-seq gene expression analysis. tm_g_boxplot boxplot module RNA-seq gene expression analysis. tm_g_forest_tte survival forest plot module analyze RNA-seq gene expression data together survival data. tm_g_km Kaplan-Meier plot module analyze RNA-seq gene expression data together survival data. tm_g_pca principal components analysis plot module RNA-seq gene expression analysis. tm_g_quality quality control module RNA-seq gene expression data. tm_g_scatterplot scatterplot module RNA-seq gene expression analysis. tm_g_volcanoplot differential gene expression analysis module.","code":""}]