Update microarray analyses: differential expression (#208)

* Start edits * There's a basic set up here * Add to snakefile and fix name * Fix jump link here * Get rid of chunk names * Switched to EnhancedVolcano and put a boxplot * Update navbar * cbethell review adds and some more EnhancedVolcano guidance * Minor edits * Add guidance on gene references and add backticks to gene reference in one place * Fix merge conflicts and then re-run everything! * Fix navbar and snakefile (rnaseq UMAP wasn't on it?) * One more tiny change. We need a head(). The results are too long for the render
AlexsLemonade · Sep 9, 2020 · 741fe25 · 741fe25
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diff --git a/01-getting-started/getting-started.html b/01-getting-started/getting-started.html
@@ -1,11 +1,10 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
 
 <head>
 
 <meta charset="utf-8" />
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
@@ -1344,7 +1343,6 @@
 }
 img {
   max-width:100%;
-  height: auto;
 }
 .tabbed-pane {
   padding-top: 12px;
@@ -1493,6 +1491,7 @@
   border: none;
   display: inline-block;
   border-radius: 4px;
+  background-color: transparent;
 }
 
 .tabset-dropdown > .nav-tabs.nav-tabs-open > li {
@@ -1521,6 +1520,12 @@
 }
 }
 
+@media print {
+.toc-content {
+  /* see https://github.com/w3c/csswg-drafts/issues/4434 */
+  float: right;
+}
+}
 
 .toc-content {
   padding-left: 30px;
@@ -1610,6 +1615,9 @@
           <ul class="dropdown-menu">
             <!-- Individual microarray pages go in this list -->
             <li><a href="../02-microarray/00-intro-to-microarray.html">Introduction</a></li>
+            <li><a href="../02-microarray/clustering_microarray_01_heatmap.html">Clustering and Heatmaps</a></li>
+            <li><a href="../02-microarray/differential-expression_microarray_01.html">Differential Expression</a></li>
+            <li><a href="../02-microarray/dimension-reduction_microarray_01_pca.html">Dimension Reduction - PCA</a></li>
             <li><a href="../02-microarray/dimension-reduction_microarray_02_umap.html">Dimension Reduction - UMAP</a></li>
 
           </ul>
@@ -1623,7 +1631,8 @@
             <li><a href="../03-rnaseq/00-intro-to-rnaseq.html">Introduction</a></li>
             <li><a href="../03-rnaseq/clustering-rnaseq_01_heatmap.html">Clustering and Heatmaps</a></li>
             <li><a href="../03-rnaseq/differential-expression_rnaseq_01.html">Differential Expression</a></li>
-            <li><a href="../03-rnaseq/dimension-reduction_rnaseq_01_pca.html">Dimension Reduction: PCA</a></li>
+            <li><a href="../03-rnaseq/dimension-reduction_rnaseq_01_pca.html">Dimension Reduction - PCA</a></li>
+            <li><a href="../03-rnaseq/dimension-reduction_rnaseq_02_umap.html">Dimension Reduction - UMAP</a></li>
 
           </ul>
         </li><!--/rna-seq dropdown-->
@@ -1829,7 +1838,7 @@ <h2>References</h2>
       theme: "bootstrap3",
       context: '.toc-content',
       hashGenerator: function (text) {
-        return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
+        return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
       },
       ignoreSelector: ".toc-ignore",
       scrollTo: 0

diff --git a/02-microarray/00-intro-to-microarray.html b/02-microarray/00-intro-to-microarray.html
@@ -1615,6 +1615,10 @@
           <ul class="dropdown-menu">
             <!-- Individual microarray pages go in this list -->
             <li><a href="../02-microarray/00-intro-to-microarray.html">Introduction</a></li>
+            <li><a href="../02-microarray/clustering_microarray_01_heatmap.html">Clustering and Heatmaps</a></li>
+            <li><a href="../02-microarray/differential-expression_microarray_01.html">Differential Expression</a></li>
+            <li><a href="../02-microarray/dimension-reduction_microarray_01_pca.html">Dimension Reduction - PCA</a></li>
+            <li><a href="../02-microarray/dimension-reduction_microarray_02_umap.html">Dimension Reduction - UMAP</a></li>
 
           </ul>
         </li> <!--/microarray dropdown-->
@@ -1625,7 +1629,10 @@
           <ul class="dropdown-menu">
             <!-- Individual RNA-Seq pages go in this list -->
             <li><a href="../03-rnaseq/00-intro-to-rnaseq.html">Introduction</a></li>
-            <li><a href="../03-rnaseq/clustering_rnaseq_01_heatmap.html">Clustering and Heatmaps</a></li>
+            <li><a href="../03-rnaseq/clustering-rnaseq_01_heatmap.html">Clustering and Heatmaps</a></li>
+            <li><a href="../03-rnaseq/differential-expression_rnaseq_01.html">Differential Expression</a></li>
+            <li><a href="../03-rnaseq/dimension-reduction_rnaseq_01_pca.html">Dimension Reduction - PCA</a></li>
+            <li><a href="../03-rnaseq/dimension-reduction_rnaseq_02_umap.html">Dimension Reduction - UMAP</a></li>
 
           </ul>
         </li><!--/rna-seq dropdown-->

diff --git a/02-microarray/clustering_microarray_01_heatmap.html b/02-microarray/clustering_microarray_01_heatmap.html