Skip to content

Commit

Permalink
update github docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@alexthiery
alexthiery committed May 12, 2023
1 parent 46320e3 commit b28122f
Show file tree
Hide file tree
Showing 3 changed files with 9 additions and 3 deletions.
2 changes: 1 addition & 1 deletion docs/_site/atom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<title>Otic reprogramming</title>
<link href="https://alexthiery.github.io/otic-reprogramminghttps://alexthiery.github.io/otic-reprogramming/atom.xml" rel="self"/>
<link href="https://alexthiery.github.io/otic-reprogramminghttps://alexthiery.github.io/otic-reprogramming/"/>
<updated>2023-03-09T06:53:39-06:00</updated>
<updated>2023-05-12T06:19:56-05:00</updated>
<id>https://alexthiery.github.io/otic-reprogramming</id>
<author>
<name>Alex Thiery</name>
Expand Down
5 changes: 4 additions & 1 deletion docs/_site/downstream/lmx1a_downstream/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -505,7 +505,10 @@ <h3 id="r-analysis-pipeline">R analysis pipeline</h3>
</br>
<p>Subset differentially expressed transcription factors based on GO terms ('GO:0003700', 'GO:0043565', 'GO:0000981').</p>
<div class="language-R highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="c1"># Get biomart GO annotations for TFs</span><span class="w">
</span><span class="n">ensembl</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">useMart</span><span class="p">(</span><span class="s2">"ensembl"</span><span class="p">,</span><span class="n">dataset</span><span class="o">=</span><span class="s2">"ggallus_gene_ensembl"</span><span class="p">)</span><span class="w">
</span><span class="n">ensembl</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">useEnsembl</span><span class="p">(</span><span class="n">biomart</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ensembl'</span><span class="p">,</span><span class="w">
</span><span class="n">dataset</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ggallus_gene_ensembl'</span><span class="p">,</span><span class="w">
</span><span class="n">version</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">104</span><span class="p">)</span><span class="w">

</span><span class="n">TF_subset</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">getBM</span><span class="p">(</span><span class="n">attributes</span><span class="o">=</span><span class="nf">c</span><span class="p">(</span><span class="s2">"ensembl_gene_id"</span><span class="p">,</span><span class="w"> </span><span class="s2">"go_id"</span><span class="p">,</span><span class="w"> </span><span class="s2">"name_1006"</span><span class="p">,</span><span class="w"> </span><span class="s2">"namespace_1003"</span><span class="p">),</span><span class="w">
</span><span class="n">filters</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ensembl_gene_id'</span><span class="p">,</span><span class="w">
</span><span class="n">values</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">rownames</span><span class="p">(</span><span class="n">res_sub</span><span class="p">),</span><span class="w">
Expand Down
5 changes: 4 additions & 1 deletion docs/_site/downstream/sox8_downstream/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -514,7 +514,10 @@ <h3 id="r-analysis-pipeline">R analysis pipeline</h3>
</br>
<p>Subset differentially expressed transcription factors based on GO terms ('GO:0003700', 'GO:0043565', 'GO:0000981').</p>
<div class="language-R highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="c1"># Get biomart GO annotations for TFs</span><span class="w">
</span><span class="n">ensembl</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">useMart</span><span class="p">(</span><span class="s2">"ensembl"</span><span class="p">,</span><span class="n">dataset</span><span class="o">=</span><span class="s2">"ggallus_gene_ensembl"</span><span class="p">)</span><span class="w">
</span><span class="n">ensembl</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">useEnsembl</span><span class="p">(</span><span class="n">biomart</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ensembl'</span><span class="p">,</span><span class="w">
</span><span class="n">dataset</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ggallus_gene_ensembl'</span><span class="p">,</span><span class="w">
</span><span class="n">version</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">104</span><span class="p">)</span><span class="w">

</span><span class="n">TF_subset</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">getBM</span><span class="p">(</span><span class="n">attributes</span><span class="o">=</span><span class="nf">c</span><span class="p">(</span><span class="s2">"ensembl_gene_id"</span><span class="p">,</span><span class="w"> </span><span class="s2">"go_id"</span><span class="p">,</span><span class="w"> </span><span class="s2">"name_1006"</span><span class="p">,</span><span class="w"> </span><span class="s2">"namespace_1003"</span><span class="p">),</span><span class="w">
</span><span class="n">filters</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s1">'ensembl_gene_id'</span><span class="p">,</span><span class="w">
</span><span class="n">values</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">rownames</span><span class="p">(</span><span class="n">res_sub</span><span class="p">),</span><span class="w">
Expand Down

0 comments on commit b28122f

Please sign in to comment.