Deploying to gh-pages from @ 8f8fe67 🚀

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 10:34 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>
+drwxr-xr-x 2 runner docker  4096 Oct  7 10:56 data
+drwxr-xr-x 2 runner docker  4096 Oct  7 10:56 images
+-rw-r--r-- 1 runner docker  1597 Oct  7 10:56 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct  7 10:56 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69876 Oct  7 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct  7 10:56 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct  7 10:56 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct  7 10:56 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct  7 10:58 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 10:34 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>
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:56 data
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:56 images
+-rw-r--r-- 1 runner docker 1.6K Oct  7 10:56 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  7 10:56 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  7 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  7 10:56 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  7 10:56 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:56 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:58 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 10:37 .
-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>
+drwxr-xr-x 4 runner docker 4.0K Oct  7 10:58 .
+drwxr-xr-x 5 runner docker 4.0K Oct  7 10:58 ..
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:56 data
+drwxr-xr-x 2 runner docker 4.0K Oct  7 10:56 images
+-rw-r--r-- 1 runner docker 1.6K Oct  7 10:56 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  7 10:56 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  7 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  7 10:56 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  7 10:56 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:56 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  7 10:58 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

@@ -417,8 +417,8 @@ <h2>🐸 Aim</h2>
 <div>
 <ul>
 <li class="fragment"><p>find genes important in frog development</p></li>
-<li class="fragment"><p>Important means genes that are differentially expressed between the control and the FGF treated sibling</p></li>
-<li class="fragment"><p>Differentially expressed means the expression on one group is significantly higher than the other</p></li>
+<li class="fragment"><p>Important means the genes that are differentially expressed between the control-treated and the FGF-treated siblings</p></li>
+<li class="fragment"><p>Differentially expressed means the expression in one group is significantly higher than in the other</p></li>
 </ul>
 </div>
 </section>
@@ -453,7 +453,7 @@ <h2 data-id="quarto-animate-title">🐭 Experimental design</h2>
 <img data-src="images/88H-exp-design-jillian.png" width="200" class="r-stretch quarto-figure-left"><p class="caption">Schematic of stem cell experiment</p><div>
 <ul>
 <li class="fragment"><p>There are three cell types: LT-HSCs, HSPCs, Progs <span style="color:#009900">These are the “treaments”</span></p></li>
-<li class="fragment"><p>Many cells of each cell type were sequenced: <span style="color:#009900">These are the replicates</span></p></li>
+<li class="fragment"><p>Many cells of each type were sequenced: <span style="color:#009900">These are the replicates</span></p></li>
 <li class="fragment"><p><span style="color:#009900">155 LT-HSCs, 701 HSPCs, 798 Progs</span></p></li>
 </ul>
 </div>
@@ -464,7 +464,7 @@ <h2>🐭 Aim</h2>
 <ul>
 <li class="fragment"><p>find genes for cell surface proteins that are important in stem cell identity</p></li>
 <li class="fragment"><p>Important means genes that are differentially expressed between at least two cell types</p></li>
-<li class="fragment"><p>Differentially expressed means the expression on one group is significantly higher than the other</p></li>
+<li class="fragment"><p>Differentially expressed means the expression in one group is significantly higher than in the other</p></li>
 </ul>
 </div>
 </section>
@@ -494,12 +494,24 @@ <h2>Raw Sequence data</h2>
 <li class="fragment">Short-read technologies e.g.&nbsp;Illumina have higher base accuracy but are harder to align</li>
 <li class="fragment">Long-read technologies e.g.&nbsp;Nanopore have lower base accuracy but are easier to align</li>
 </ul></li>
+</ul>
+</div>
+</section></section>
+<section>
+<section id="the-raw-data-1" class="title-slide slide level1 center">
+<h1>The raw data</h1>
+
+</section>
+<section id="raw-sequence-data-1" class="slide level2">
+<h2>Raw Sequence data</h2>
+<div>
+<ul>
 <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="#/references" role="doc-biblioref" onclick="">Rand and Forrester 2022</a>)</span></p></li>
 </ul>
 </div>
 </section>
-<section id="raw-sequence-data-1" class="slide level2">
+<section id="raw-sequence-data-2" class="slide level2">
 <h2>Raw Sequence data</h2>
 <div>
 <ul>