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Plant-Food-Research-Open · Mar 28, 2024 · b7c8c76 · b7c8c76
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diff --git a/_quarto.yml b/_quarto.yml
@@ -6,16 +6,16 @@ book:
   title: "The `moiraine` R package user manual"
   author: "Olivia Angelin-Bonnet"
   search: true
-  site-url: https://solid-lamp-kq546rq.pages.github.io/
+  site-url: https://plant-food-research-open.github.io/moiraine-manual/
   sharing: [twitter]
   sidebar:
     tools:
       - icon: github
         menu:
           - text: Manual source code
-            url: https://github.com/PlantandFoodResearch/moiraine-manual
+            url: https://github.com/Plant-Food-Research-Open/moiraine-manual
           - text: Package source code
-            url: https://github.com/PlantandFoodResearch/moiraine
+            url: https://github.com/Plant-Food-Research-Open/moiraine
   chapters:
     - index.qmd
     - overview.qmd

diff --git a/docs/comparison.html b/docs/comparison.html
@@ -137,12 +137,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">14</span>&nb
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/comparison_files/figure-html/plot-features-weight-average-1.png b/docs/comparison_files/figure-html/plot-features-weight-average-1.png
diff --git a/docs/comparison_files/figure-html/plot-features-weight-pair-1.png b/docs/comparison_files/figure-html/plot-features-weight-pair-1.png
diff --git a/docs/comparison_files/figure-html/plot-features-weight-raw-1.png b/docs/comparison_files/figure-html/plot-features-weight-raw-1.png
diff --git a/docs/comparison_files/figure-html/plot-features_weight-pair-mofa-1.png b/docs/comparison_files/figure-html/plot-features_weight-pair-mofa-1.png
diff --git a/docs/data_import.html b/docs/data_import.html
@@ -156,12 +156,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">3</span>&nbs
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/diablo.html b/docs/diablo.html
@@ -137,12 +137,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">11</span>&nb
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/evaluation.html b/docs/evaluation.html
@@ -156,12 +156,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">13</span>&nb
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/example_dataset.html b/docs/example_dataset.html
@@ -107,12 +107,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span>&nbs
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>
@@ -310,7 +310,7 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="omics-analyses"><span cla
 </section>
 <section id="data-processing" class="level2" data-number="2.3">
 <h2 data-number="2.3" class="anchored" data-anchor-id="data-processing"><span class="header-section-number">2.3</span> Data processing</h2>
-<p>The full script for the data processing can be found in the <a href="https://github.com/PlantandFoodResearch/moiraine/blob/main/data-raw/example_dataset_li2022.R"><code>moiraine</code> GitHub repository</a>.</p>
+<p>The full script for the data processing can be found in the <a href="https://github.com/Plant-Food-Research-Open/moiraine/blob/main/data-raw/example_dataset_li2022.R"><code>moiraine</code> GitHub repository</a>.</p>
 <section id="genomics-dataset" class="level3" data-number="2.3.1">
 <h3 data-number="2.3.1" class="anchored" data-anchor-id="genomics-dataset"><span class="header-section-number">2.3.1</span> Genomics dataset</h3>
 <p>The matrix of SNP dosage and table of SNP information were downloaded from the <a href="https://doi.org/10.5683/SP3/ZETWNY">borealis database</a>. The list of significant QTLs and eQTLs was extracted from the <a href="https://figshare.com/articles/dataset/DataSheet1_Applying_multi-omics_data_to_study_the_genetic_background_of_bovine_respiratory_disease_infection_in_feedlot_crossbred_cattle_xlsx/21708890">supplementary file</a> made available on Figshare alongside the article and completed with information from Table 1 from <span class="citation" data-cites="li2022">Li et al. (<a href="references.html#ref-li2022" role="doc-biblioref">2022</a>)</span>. Note that some of the QTLs and eQTLs listed in the article and supplementary material were obtained from the RNAseq dataset, and so are not present in the version of the dataset used for the present tutorial. If a SNP was selected as both QTL and eQTL, only the results yielding the smallest FDR value were retained.</p>

diff --git a/docs/index.html b/docs/index.html
@@ -137,12 +137,12 @@ <h1 class="quarto-secondary-nav-title">The <code>moiraine</code> R package user
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/inspecting_multidataset.html b/docs/inspecting_multidataset.html
@@ -137,12 +137,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">4</span>&nbs
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/interpretation.html b/docs/interpretation.html
@@ -137,12 +137,12 @@ <h1 class="quarto-secondary-nav-title"><span class="chapter-number">12</span>&nb
     <a href="" title="" id="sidebar-tool-dropdown-0" class="sidebar-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-github"></i></a>
     <ul class="dropdown-menu" aria-labelledby="sidebar-tool-dropdown-0">
 <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine-manual">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine-manual">
           Manual source code
           </a>
         </li>
         <li>
-          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/PlantandFoodResearch/moiraine">
+          <a class="dropdown-item sidebar-tools-main-item" href="https://github.com/Plant-Food-Research-Open/moiraine">
           Package source code
           </a>
         </li>

diff --git a/docs/interpretation_files/figure-html/diablo-features-weight-pair-1.png b/docs/interpretation_files/figure-html/diablo-features-weight-pair-1.png
diff --git a/docs/interpretation_files/figure-html/mofa-features-weight-pair-1.png b/docs/interpretation_files/figure-html/mofa-features-weight-pair-1.png
diff --git a/docs/interpretation_files/figure-html/so2pls-features-weight-pair-1.png b/docs/interpretation_files/figure-html/so2pls-features-weight-pair-1.png
diff --git a/docs/interpretation_files/figure-html/spls-features-weight-pair-1.png b/docs/interpretation_files/figure-html/spls-features-weight-pair-1.png