Update CD4 examples

examples/Salomon/CD4/reports/MOFA/README.mkdn

@@ -0,0 +1,18 @@
+[MOFA](https://github.com/PMBio/MOFA) was used to analyze RNA-seq data
+and ChIP-seq data for 3 histone marks together, looking for sources of
+variation shared acorss all data types. Two different analyses were
+done, one with ChIP-seq reads counted in promoter regions, and one
+with ChIP-seq reads counted in called peaks. Each analysis is split
+into two steps. The first step ("run") is fitting the model (which
+takes a long time) and performing some basic QC, while the second step
+("analyze") loads the fitted model and performs some analysis.
+
+## Peak-based analysis
+
+- Step 1: [`peak-mofa-run.html`](peak-mofa-run.html)
+- Step 2: [`peak-mofa-analyze.html`](peak-mofa-analyze.html)
+
+## Promoter-based analysis
+
+- Step 1: [`promoter-mofa-run.html`](promoter-mofa-run.html)
+- Step 2: [`promoter-mofa-analyze.html`](promoter-mofa-analyze.html)

examples/Salomon/CD4/reports/MOFA/index.html

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+<p><a href="https://github.com/PMBio/MOFA">MOFA</a> was used to analyze RNA-seq data and ChIP-seq data for 3 histone marks together, looking for sources of variation shared acorss all data types. Two different analyses were done, one with ChIP-seq reads counted in promoter regions, and one with ChIP-seq reads counted in called peaks. Each analysis is split into two steps. The first step (“run”) is fitting the model (which takes a long time) and performing some basic QC, while the second step (“analyze”) loads the fitted model and performs some analysis.</p>
+<h2 id="peak-based-analysis">Peak-based analysis</h2>
+<ul>
+<li>Step 1: <a href="peak-mofa-run.html"><code>peak-mofa-run.html</code></a></li>
+<li>Step 2: <a href="peak-mofa-analyze.html"><code>peak-mofa-analyze.html</code></a></li>
+</ul>
+<h2 id="promoter-based-analysis">Promoter-based analysis</h2>
+<ul>
+<li>Step 1: <a href="promoter-mofa-run.html"><code>promoter-mofa-run.html</code></a></li>
+<li>Step 2: <a href="promoter-mofa-analyze.html"><code>promoter-mofa-analyze.html</code></a></li>
+</ul>

examples/Salomon/CD4/reports/README.mkdn

@@ -1,2 +1,4 @@
 - [`ChIP-seq`](ChIP-seq): Example reports for ChIP-seq data
 - [`RNA-seq`](RNA-seq): Example reports for RNA-seq data
+- [`MOFA`](MOFA): Example reports for multi-omics factor analysis of
+  ChIP-seq and RNA-seq together

examples/Salomon/CD4/reports/index.html

@@ -1,4 +1,5 @@
 <ul>
 <li><a href="ChIP-seq"><code>ChIP-seq</code></a>: Example reports for ChIP-seq data</li>
 <li><a href="RNA-seq"><code>RNA-seq</code></a>: Example reports for RNA-seq data</li>
+<li><a href="MOFA"><code>MOFA</code></a>: Example reports for multi-omics factor analysis of ChIP-seq and RNA-seq together</li>
 </ul>