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diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html
@@ -425,49 +425,49 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 136
-drwxr-xr-x 2 runner docker  4096 Oct 15 09:00 data
-drwxr-xr-x 2 runner docker  4096 Oct 15 09:00 images
--rw-r--r-- 1 runner docker  1597 Oct 15 09:00 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct 15 09:00 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69877 Oct 15 09:04 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct 15 09:00 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct 15 09:00 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct 15 09:00 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct 15 09:05 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct 15 09:26 data
+drwxr-xr-x 2 runner docker  4096 Oct 15 09:26 images
+-rw-r--r-- 1 runner docker  1597 Oct 15 09:26 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct 15 09:26 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69877 Oct 15 09:29 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct 15 09:26 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct 15 09:26 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct 15 09:26 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct 15 09:29 workshop.rmarkdown</code></pre>
 </div>
 </div>
 <p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 136K
-drwxr-xr-x 2 runner docker 4.0K Oct 15 09:00 data
-drwxr-xr-x 2 runner docker 4.0K Oct 15 09:00 images
--rw-r--r-- 1 runner docker 1.6K Oct 15 09:00 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct 15 09:00 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct 15 09:04 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct 15 09:00 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 15 09:00 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 15 09:00 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 15 09:05 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct 15 09:26 data
+drwxr-xr-x 2 runner docker 4.0K Oct 15 09:26 images
+-rw-r--r-- 1 runner docker 1.6K Oct 15 09:26 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 15 09:26 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct 15 09:29 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct 15 09:26 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 15 09:26 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 15 09:26 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 15 09:29 workshop.rmarkdown</code></pre>
 </div>
 </div>
 <p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 144K
-drwxr-xr-x 4 runner docker 4.0K Oct 15 09:05 .
-drwxr-xr-x 5 runner docker 4.0K Oct 15 09:04 ..
-drwxr-xr-x 2 runner docker 4.0K Oct 15 09:00 data
-drwxr-xr-x 2 runner docker 4.0K Oct 15 09:00 images
--rw-r--r-- 1 runner docker 1.6K Oct 15 09:00 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct 15 09:00 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct 15 09:04 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct 15 09:00 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 15 09:00 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 15 09:00 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 15 09:05 workshop.rmarkdown</code></pre>
+drwxr-xr-x 4 runner docker 4.0K Oct 15 09:29 .
+drwxr-xr-x 5 runner docker 4.0K Oct 15 09:29 ..
+drwxr-xr-x 2 runner docker 4.0K Oct 15 09:26 data
+drwxr-xr-x 2 runner docker 4.0K Oct 15 09:26 images
+-rw-r--r-- 1 runner docker 1.6K Oct 15 09:26 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 15 09:26 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct 15 09:29 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct 15 09:26 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 15 09:26 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 15 09:26 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 15 09:29 workshop.rmarkdown</code></pre>
 </div>
 </div>
 <p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>

diff --git a/omics/omics.html b/omics/omics.html
@@ -21,7 +21,26 @@
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   vertical-align: middle;
 }
-</style>
+/* CSS for citations */
+div.csl-bib-body { }
+div.csl-entry {
+  clear: both;
+}
+.hanging-indent div.csl-entry {
+  margin-left:2em;
+  text-indent:-2em;
+}
+div.csl-left-margin {
+  min-width:2em;
+  float:left;
+}
+div.csl-right-inline {
+  margin-left:2em;
+  padding-left:1em;
+}
+div.csl-indent {
+  margin-left: 2em;
+}</style>
 
 
 <script src="../site_libs/quarto-nav/quarto-nav.js"></script>
@@ -287,49 +306,44 @@ <h2 class="anchored" data-anchor-id="omics-1-hello-data">Omics 1: 👋 Hello dat
 </section>
 <section id="omics-2-statistical-analysis" class="level2">
 <h2 class="anchored" data-anchor-id="omics-2-statistical-analysis">Omics 2: Statistical Analysis</h2>
-<p>before</p>
-<ul>
-<li>which genes matter: expression, DE</li>
-<li>goal of DE</li>
-<li>how does DE work</li>
-<li>multiple testing: FDR</li>
-<li>say what comparisons we will do</li>
-</ul>
-<p>workshop - open project import the data - revise! - prep for DE - lists of genes - writing to files</p>
-<p>after</p>
-<ul>
-<li>document what you have done</li>
-<li>repeat on another comparison</li>
-</ul>
+<p>This week we cover differential expression analysis on raw counts or log normalised values. The independent study will allow you to check you have what you should have following the <a href="week-3/workshop.html">Omics 1: Hello Data workshop</a> and <a href="week-3/study_after_workshop.html">Consolidation study</a>. It will also summarise the concepts and methods we will use in the workshop. In the workshop, you will learn how to perform differential expression analysis on raw counts using <strong><code>DESeq2</code></strong> <span class="citation" data-cites="DESeq2">(<a href="#ref-DESeq2" role="doc-biblioref">Love, Huber, and Anders 2014</a>)</span> or on logged normalised expression values using <strong><code>scran</code></strong> <span class="citation" data-cites="scran">(<a href="#ref-scran" role="doc-biblioref">Lun, McCarthy, and Marioni 2016</a>)</span> or both.</p>
 </section>
 <section id="omics-3-visualising-and-interpreting" class="level2">
 <h2 class="anchored" data-anchor-id="omics-3-visualising-and-interpreting">Omics 3: Visualising and Interpreting</h2>
 <p>before</p>
 <ul>
 <li>recap what we have</li>
+<li>PCA</li>
 <li>volcano plot described</li>
 <li>GO terms</li>
 <li></li>
 </ul>
 <p>workshop</p>
 <ul>
-<li>open project import the data</li>
-<li>revise!</li>
+<li>PCA</li>
 <li>volcano plot</li>
-<li>kable table? knitr::kable(df) |&gt; kableExtra::kable_styling()</li>
 <li>annotating with go terms</li>
 </ul>
 <p>after</p>
 <ul>
 <li>document what you have done</li>
 <li>repeat on another comparison</li>
 </ul>
+<p>References</p>
+
 
 
 </section>
 </section>
 
-</main> <!-- /main -->
+<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" role="list">
+<div id="ref-DESeq2" class="csl-entry" role="listitem">
+Love, Michael I., Wolfgang Huber, and Simon Anders. 2014. <span>“Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2”</span> 15: 550. <a href="https://doi.org/10.1186/s13059-014-0550-8">https://doi.org/10.1186/s13059-014-0550-8</a>.
+</div>
+<div id="ref-scran" class="csl-entry" role="listitem">
+Lun, Aaron T. L., Davis J. McCarthy, and John C. Marioni. 2016. <span>“A Step-by-Step Workflow for Low-Level Analysis of Single-Cell RNA-Seq Data with Bioconductor”</span> 5: 2122. <a href="https://doi.org/10.12688/f1000research.9501.2">https://doi.org/10.12688/f1000research.9501.2</a>.
+</div>
+</div></section></div></main> <!-- /main -->
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