Deploying to gh-pages from @ a1b7932 🚀

core/week-2/workshop.html

@@ -424,46 +424,46 @@ <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 64
-drwxr-xr-x 2 runner docker  4096 Oct 23 15:06 data
-drwxr-xr-x 2 runner docker  4096 Oct 23 15:06 images
--rw-r--r-- 1 runner docker  1597 Oct 23 15:06 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct 23 15:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Oct 23 15:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct 23 15:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct 23 15:06 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct 23 15:08 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct 23 16:29 data
+drwxr-xr-x 2 runner docker  4096 Oct 23 16:29 images
+-rw-r--r-- 1 runner docker  1597 Oct 23 16:29 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct 23 16:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  4807 Oct 23 16:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct 23 16:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct 23 16:29 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct 23 16:32 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 64K
-drwxr-xr-x 2 runner docker 4.0K Oct 23 15:06 data
-drwxr-xr-x 2 runner docker 4.0K Oct 23 15:06 images
--rw-r--r-- 1 runner docker 1.6K Oct 23 15:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct 23 15:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Oct 23 15:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 23 15:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 23 15:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 23 15:08 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct 23 16:29 data
+drwxr-xr-x 2 runner docker 4.0K Oct 23 16:29 images
+-rw-r--r-- 1 runner docker 1.6K Oct 23 16:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 23 16:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Oct 23 16:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 23 16:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 23 16:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 23 16:32 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 72K
-drwxr-xr-x 4 runner docker 4.0K Oct 23 15:08 .
-drwxr-xr-x 5 runner docker 4.0K Oct 23 15:06 ..
-drwxr-xr-x 2 runner docker 4.0K Oct 23 15:06 data
-drwxr-xr-x 2 runner docker 4.0K Oct 23 15:06 images
--rw-r--r-- 1 runner docker 1.6K Oct 23 15:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct 23 15:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Oct 23 15:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 23 15:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 23 15:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 23 15:08 workshop.rmarkdown</code></pre>
+drwxr-xr-x 4 runner docker 4.0K Oct 23 16:32 .
+drwxr-xr-x 5 runner docker 4.0K Oct 23 16:29 ..
+drwxr-xr-x 2 runner docker 4.0K Oct 23 16:29 data
+drwxr-xr-x 2 runner docker 4.0K Oct 23 16:29 images
+-rw-r--r-- 1 runner docker 1.6K Oct 23 16:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 23 16:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Oct 23 16:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 23 16:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 23 16:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 23 16:32 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-5/overview.html

@@ -277,7 +277,7 @@ <h1 class="title">Overview</h1>
 
 </header>
 
-<p>This week we cover how to visualise and interpret the results of your differential expression analysis. The independent study will allow you to check you have what you should have following the <a href="../week-4/workshop.html">Omics 2: Statistical Analysis workshop</a> and <a href="../week-4/study_after_workshop.html">Consolidation study</a>. It will also summarise the the methods and plots we will go through in the workshop. In the workshop, we will learn how to conduct a Principle Component Analysis (PCA) and plot the results as well as how to create a nicely formatted Volcano plot and heatmap.</p>
+<p>This week we cover how to visualise and interpret the results of your differential expression analysis. The independent study will allow you to check you have what you should have following the <a href="../week-4/workshop.html">Omics 2: Statistical Analysis workshop</a> and <a href="../week-4/study_after_workshop.html">Consolidation study</a>. It will also summarise the the methods and plots we will go through in the workshop. In the workshop, we will learn how to merge gene information into out results, conduct a Principle Component Analysis (PCA) and plot the results as well as how to create a nicely formatted Volcano plot and heatmap.</p>
 <p>We suggest you sit together with your group in the workshop.</p>
 <section id="learning-objectives" class="level3">
 <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>

omics/week-5/study_before_workshop.html

@@ -503,8 +503,16 @@
 <li>a gene id</li>
 </ul></section><section id="frogs-1" class="slide level2"><h2>🐸 Frogs</h2>
 <div class="cell">
-<div class="cell-output cell-output-error">
-<pre><code>Error: 'results/s30_results.csv' does not exist in current working directory ('/home/runner/work/BIO00088H-data/BIO00088H-data/omics/week-5').</code></pre>
+<div class="cell-output cell-output-stdout">
+<pre><code>Rows: 10,136
+Columns: 7
+$ baseMean        &lt;dbl&gt; 237.553928, 531.565700, 86.392830, 49.813502, 419.9983…
+$ log2FoldChange  &lt;dbl&gt; 0.096601855, -0.089588528, -0.192811203, -0.008858703,…
+$ lfcSE           &lt;dbl&gt; 0.2079396, 0.1557384, 0.3253216, 0.4342614, 0.1685420,…
+$ stat            &lt;dbl&gt; 0.46456683, -0.57525007, -0.59267874, -0.02039947, -0.…
+$ pvalue          &lt;dbl&gt; 0.64224169, 0.56512218, 0.55339617, 0.98372471, 0.8699…
+$ padj            &lt;dbl&gt; 0.9998970, 0.9998970, 0.9998970, 0.9998970, 0.9998970,…
+$ xenbase_gene_id &lt;chr&gt; "XB-GENE-1000007", "XB-GENE-1000023", "XB-GENE-1000062…</code></pre>
 </div>
 </div>
 <div class="fragment">
@@ -708,7 +716,7 @@
 <li><p>The 🐭 mouse data were already log<sub>2</sub>normalised</p></li>
 <li><p>The 🐸 frog data were normalised by the DE method and saved to file. We will log<sub>2</sub> transform before doing visualisations</p></li>
 </ul></section><section id="packages-to-install-before-the-workshop" class="slide level2"><h2>Packages to install before the workshop</h2>
-<p><strong><code>heatmaply</code></strong> <span class="citation" data-cites="heatmapply">(<a href="#/references" role="doc-biblioref" onclick=""><strong>heatmapply?</strong></a>)</span> and <strong><code>ggrepel</code></strong> <span class="citation" data-cites="ggrepel">(<a href="#/references" role="doc-biblioref" onclick="">Slowikowski 2023</a>)</span> from CRAN in the the normal way:</p>
+<p><strong><code>heatmaply</code></strong> <span class="citation" data-cites="heatmaply">(<a href="#/references" role="doc-biblioref" onclick="">Galili et al. 2017</a>)</span> and <strong><code>ggrepel</code></strong> <span class="citation" data-cites="ggrepel">(<a href="#/references" role="doc-biblioref" onclick="">Slowikowski 2023</a>)</span> from CRAN in the the normal way:</p>
 <div class="cell">
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"heatmaply"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"ggrepel"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -739,6 +747,9 @@
 <div id="ref-fisher2023" class="csl-entry" role="listitem">
 Fisher, Malcolm, Christina James-Zorn, Virgilio Ponferrada, Andrew J Bell, Nivitha Sundararaj, Erik Segerdell, Praneet Chaturvedi, et al. 2023. <span>“Xenbase: Key Features and Resources of the Xenopus Model Organism Knowledgebase.”</span> <em>Genetics</em> 224 (1): iyad018. <a href="https://doi.org/10.1093/genetics/iyad018">https://doi.org/10.1093/genetics/iyad018</a>.
 </div>
+<div id="ref-heatmaply" class="csl-entry" role="listitem">
+Galili, Tal, O’Callaghan, Alan, Sidi, Jonathan, Sievert, and Carson. 2017. <span>“Heatmaply: An r Package for Creating Interactive Cluster Heatmaps for Online Publishing.”</span> <em>Bioinformatics</em>. <a href="https://doi.org/10.1093/bioinformatics/btx657">https://doi.org/10.1093/bioinformatics/btx657</a>.
+</div>
 <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>