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Add microarray gene ID conversion example #212

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merged 19 commits into from
Sep 18, 2020
Merged

Add microarray gene ID conversion example #212

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7bdd012
add microarray gene id conversion notebook
cbethell Sep 10, 2020
5a1f27b
add section to explore the mapped df and add some context
cbethell Sep 10, 2020
d39c193
add context around `multiVals`
cbethell Sep 11, 2020
2b3e324
add annotation package to dockerfile
cbethell Sep 11, 2020
58bd38c
add new reference
cbethell Sep 11, 2020
62095e0
fix a sentence
cbethell Sep 11, 2020
a4a8b38
add more context around `multiVals`
cbethell Sep 11, 2020
1c66b52
add a bit more context around the gene ids used
cbethell Sep 12, 2020
a0c076b
use `list` and `filter` in `mapIds()` function execution
cbethell Sep 15, 2020
15dbff1
fix some formatting
cbethell Sep 15, 2020
a40cbae
fix spacing
cbethell Sep 15, 2020
f4b3d68
add a sanity check after obtaining new filtered df
cbethell Sep 15, 2020
251cf96
Merge branch 'master' of https://github.com/AlexsLemonade/refinebio-e…
cbethell Sep 16, 2020
b739911
incorporate @cansavvy's review suggestions
cbethell Sep 16, 2020
5e52faf
fix typo and add step to join rest of data to final df
cbethell Sep 17, 2020
c843d29
fix link in reference file
cbethell Sep 17, 2020
0fadca7
Apply @cansavvy's suggestions from code review
cbethell Sep 17, 2020
62d29cb
add reference for `AnnotationDbi` and rerun
cbethell Sep 17, 2020
1613e8f
fix order in `references.bib`
cbethell Sep 17, 2020
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14 changes: 5 additions & 9 deletions 01-getting-started/getting-started.html
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<!DOCTYPE html>

<html>
<html xmlns="http://www.w3.org/1999/xhtml">

<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" />

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}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
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border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}

.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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}
}

@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}

.toc-content {
padding-left: 30px;
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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>

</ul>
</li> <!--/microarray dropdown-->
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theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
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14 changes: 5 additions & 9 deletions 02-microarray/00-intro-to-microarray.html
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@@ -1,10 +1,11 @@
<!DOCTYPE html>

<html>
<html xmlns="http://www.w3.org/1999/xhtml">

<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" />

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}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
Expand Down Expand Up @@ -1491,7 +1493,6 @@
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}

.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
Expand Down Expand Up @@ -1520,12 +1521,6 @@
}
}

@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}

.toc-content {
padding-left: 30px;
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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>

</ul>
</li> <!--/microarray dropdown-->
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theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
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67 changes: 29 additions & 38 deletions 02-microarray/clustering_microarray_01_heatmap.html
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71 changes: 31 additions & 40 deletions 02-microarray/dimension-reduction_microarray_01_pca.html
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79 changes: 35 additions & 44 deletions 02-microarray/dimension-reduction_microarray_02_umap.html
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