Deploying to gh-pages from @ 6070e50 🚀

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  7 10:21 data
-drwxr-xr-x 2 runner docker  4096 Oct  7 10:21 images
--rw-r--r-- 1 runner docker  1597 Oct  7 10:21 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  7 10:21 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  7 10:23 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  7 10:21 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  7 10:21 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct  7 10:21 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct  7 10:23 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct  7 10:34 data
+drwxr-xr-x 2 runner docker  4096 Oct  7 10:34 images
+-rw-r--r-- 1 runner docker  1597 Oct  7 10:34 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct  7 10:34 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69876 Oct  7 10:37 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct  7 10:34 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct  7 10:34 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct  7 10:34 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct  7 10:37 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  7 10:21 data
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:21 images
--rw-r--r-- 1 runner docker 1.6K Oct  7 10:21 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  7 10:21 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  7 10:23 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  7 10:21 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  7 10:21 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:21 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:23 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 data
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 images
+-rw-r--r-- 1 runner docker 1.6K Oct  7 10:34 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  7 10:34 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  7 10:37 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  7 10:34 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  7 10:34 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:34 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:37 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  7 10:23 .
-drwxr-xr-x 5 runner docker 4.0K Oct  7 10:23 ..
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:21 data
-drwxr-xr-x 2 runner docker 4.0K Oct  7 10:21 images
--rw-r--r-- 1 runner docker 1.6K Oct  7 10:21 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  7 10:21 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  7 10:23 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  7 10:21 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  7 10:21 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:21 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  7 10:23 workshop.rmarkdown</code></pre>
+drwxr-xr-x 4 runner docker 4.0K Oct  7 10:37 .
+drwxr-xr-x 5 runner docker 4.0K Oct  7 10:36 ..
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 data
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:34 images
+-rw-r--r-- 1 runner docker 1.6K Oct  7 10:34 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  7 10:34 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  7 10:37 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  7 10:34 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  7 10:34 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:34 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:37 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>

omics/week-3/study_before_workshop.html

@@ -495,7 +495,7 @@ <h2>Raw Sequence data</h2>
 <li class="fragment">Long-read technologies e.g.&nbsp;Nanopore have lower base accuracy but are easier to align</li>
 </ul></li>
 <li class="fragment"><p>Sequencing technology is constantly improving</p></li>
-<li class="fragment"><p>Optional: You can read more about Sequencing technologies in <a href="https://cloud-span.github.io/experimental_design00-overview/">Statistically useful experimental design</a> <span class="citation" data-cites="rand_statistically_2022">(<a href="#/workshops-1" role="doc-biblioref" onclick="">Rand and Forrester 2022</a>)</span></p></li>
+<li class="fragment"><p>Optional: You can read more about Sequencing technologies in <a href="https://cloud-span.github.io/experimental_design00-overview/">Statistically useful experimental design</a> <span class="citation" data-cites="rand_statistically_2022">(<a href="#/references" role="doc-biblioref" onclick="">Rand and Forrester 2022</a>)</span></p></li>
 </ul>
 </div>
 </section>
@@ -531,30 +531,33 @@ <h2>🐸 Data</h2>
 <li><p>Unpublished (so far!)</p></li>
 <li><p>Expression for the whole transcriptome <a href="https://www.xenbase.org/xenbase/static-xenbase/ftpDatafiles.jsp"><em>X. laevis</em> v10.1 genome assembly</a></p></li>
 <li><p>Values are raw counts</p></li>
-<li><p>The statistical analysis method we will use <code>DESeq2</code> <span class="citation" data-cites="DESeq2">(<a href="#/workshops-1" role="doc-biblioref" onclick="">Love, Huber, and Anders 2014</a>)</span> requires raw counts and performs the normalisation itself</p></li>
+<li><p>The statistical analysis method we will use <code>DESeq2</code> <span class="citation" data-cites="DESeq2">(<a href="#/references" role="doc-biblioref" onclick="">Love, Huber, and Anders 2014</a>)</span> requires raw counts and performs the normalisation itself</p></li>
 </ul>
 </section>
 <section id="data-1" class="slide level2">
 <h2>🐭 Data</h2>
 <ul>
-<li><p>Published in <span class="citation" data-cites="nestorowa2016">Nestorowa et al. (<a href="#/workshops-1" role="doc-biblioref" onclick="">2016</a>)</span></p></li>
+<li><p>Published in <span class="citation" data-cites="nestorowa2016">Nestorowa et al. (<a href="#/references" role="doc-biblioref" onclick="">2016</a>)</span></p></li>
 <li><p>Expression for a subset of genes, the surfaceome</p></li>
 <li><p>Values are log2 normalised values</p></li>
-<li><p>The statistical analysis method we will use <code>scran</code> <span class="citation" data-cites="scran">(<a href="#/workshops-1" role="doc-biblioref" onclick="">Lun, McCarthy, and Marioni 2016</a>)</span> requires normalised values</p></li>
+<li><p>The statistical analysis method we will use <code>scran</code> <span class="citation" data-cites="scran">(<a href="#/references" role="doc-biblioref" onclick="">Lun, McCarthy, and Marioni 2016</a>)</span> requires normalised values</p></li>
 </ul>
 </section></section>
 <section>
 <section id="workshops" class="title-slide slide level1 center">
 <h1>Workshops</h1>
 
 </section>
-<section id="workshops-1" class="slide level2 smaller scrollable">
+<section id="workshops-1" class="slide level2">
 <h2>Workshops</h2>
 <ul>
 <li><p>Omics 1: Hello data Getting to know the data. Checking the distributions of values overall, across samples and across genes to check things are as we expect and detect genes/samples that need to be removed</p></li>
 <li><p>Omics 2: Statistical Analysis Identifying which genes are differentially expressed between treatments. This is the main analysis step. We will use different methods for bulk and single cell data.</p></li>
 <li><p>Omics 3: Visualising and Interpreting Production of volcano plots and heatmaps to visualise the results of the statistical analysis. We will also look at how to interpret the results and how to find out more about the genes of interest.</p></li>
 </ul>
+</section>
+<section id="references" class="slide level2 smaller scrollable">
+<h2>References</h2>
 
 <div class="footer footer-default">
 <p>🔗 <a href="https://3mmarand.github.io/BIO00088H-data/omics/week-3/overview.html">About Omics 1: Hello data!</a></p>