Add microarray gene ID conversion example (#212)

* add microarray gene id conversion notebook - make appropriate updates to `references.bib`, `Snakefile`, and `_navbar.html` file * add section to explore the mapped df and add some context * add context around `multiVals` - add references to `references.bib` - update comments and documentation - rerun Snakefile * add annotation package to dockerfile * add new reference - rerun Snakefile * fix a sentence * add more context around `multiVals` * add a bit more context around the gene ids used - fix formatting * use `list` and `filter` in `mapIds()` function execution - rename the file and propagate change in `Snakefile` and `navbar.html` - update references - rearrange notebook and rerun Snakefile * fix some formatting * fix spacing * add a sanity check after obtaining new filtered df * incorporate @cansavvy's review suggestions * fix typo and add step to join rest of data to final df * fix link in reference file * Apply @cansavvy's suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * add reference for `AnnotationDbi` and rerun * fix order in `references.bib` Co-authored-by: Candace Savonen <cansav09@gmail.com>
AlexsLemonade · Sep 18, 2020 · d5f6c7a · d5f6c7a
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diff --git a/01-getting-started/getting-started.html b/01-getting-started/getting-started.html
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             <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>
+            <li><a href="../02-microarray/gene-id-annotation_microarray_01_ensembl.html">Ensembl Gene ID Annotation</a></li>
 
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@@ -1838,7 +1834,7 @@ <h2>References</h2>
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diff --git a/02-microarray/00-intro-to-microarray.html b/02-microarray/00-intro-to-microarray.html
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 <!DOCTYPE html>
 
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+<html xmlns="http://www.w3.org/1999/xhtml">
 
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 <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" />
 
@@ -1343,6 +1344,7 @@
 }
 img {
   max-width:100%;
+  height: auto;
 }
 .tabbed-pane {
   padding-top: 12px;
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   border: none;
   display: inline-block;
   border-radius: 4px;
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@@ -1619,6 +1614,7 @@
             <li><a href="../02-microarray/differential-expression_microarray_01.html">Differential Expression</a></li>
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             <li><a href="../02-microarray/dimension-reduction_microarray_02_umap.html">Dimension Reduction - UMAP</a></li>
+            <li><a href="../02-microarray/gene-id-annotation_microarray_01_ensembl.html">Ensembl Gene ID Annotation</a></li>
 
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diff --git a/02-microarray/clustering_microarray_01_heatmap.html b/02-microarray/clustering_microarray_01_heatmap.html
diff --git a/02-microarray/dimension-reduction_microarray_01_pca.html b/02-microarray/dimension-reduction_microarray_01_pca.html
diff --git a/02-microarray/dimension-reduction_microarray_02_umap.html b/02-microarray/dimension-reduction_microarray_02_umap.html