Deploying to gh-pages from @ 59eabb4 🚀

core/core.html

@@ -269,7 +269,7 @@ <h1 class="title">Core Data Analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-1/overview.html

@@ -266,7 +266,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-1/study_after_workshop.html

@@ -266,7 +266,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-1/study_before_workshop.html

@@ -259,7 +259,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-1/workshop.html

@@ -319,7 +319,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-2/overview.html

@@ -257,7 +257,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-2/study_after_workshop.html

@@ -257,7 +257,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-2/study_before_workshop.html

@@ -423,7 +423,7 @@
 </div>
 </div>
 
-  <p class="date">8 October, 2023</p>
+  <p class="date">13 October, 2023</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited

core/week-2/workshop.html

@@ -339,7 +339,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 
@@ -360,7 +360,7 @@ <h1 class="title">Workshop</h1>
 </ul></section><section id="images" class="level2"><h2 class="anchored" data-anchor-id="images">Images</h2>
 <p><a href="data/control_merged.tif">control_merged.tif</a></p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://docs.ropensci.org/ijtiff/">ijtiff</a></span><span class="op">)</span></span>
-<span><span class="va">img</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://docs.ropensci.org/ijtiff/reference/read_tif.html">read_tif</a></span><span class="op">(</span><span class="st">"data/control_merged.tif"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="va">img</span> <span class="op">&lt;-</span> <span class="fu">read_tif</span><span class="op">(</span><span class="st">"data/control_merged.tif"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">img</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <ul>
 <li><p>an image at least one and usually more matrices of numbers representing the intensity of light at each pixel in the image</p></li>
@@ -369,7 +369,7 @@ <h1 class="title">Workshop</h1>
 <li><p>a frame is a single image in a series of images</p></li>
 <li><p>we might normally call this a multi-dimensional array: x and y coordinates of the pixels are 2 dimensions, the channel is the third dimension and time is the forth dimension</p></li>
 </ul>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://docs.ropensci.org/ijtiff/reference/display.html">display</a></span><span class="op">(</span><span class="va">img</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">display</span><span class="op">(</span><span class="va">img</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section><section id="structure" class="level2"><h2 class="anchored" data-anchor-id="structure">Structure</h2>
 <p><a href="data/1cq2.pdb">1cq2.pdb</a></p>
 </section></section><section id="workflow-tips" class="level1"><h1>Workflow tips</h1>
@@ -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  8 10:06 data
-drwxr-xr-x 2 runner docker  4096 Oct  8 10:06 images
--rw-r--r-- 1 runner docker  1597 Oct  8 10:06 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  8 10:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  8 10:09 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  8 10:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  8 10:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct  8 10:06 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct  8 10:09 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct 13 10:44 data
+drwxr-xr-x 2 runner docker  4096 Oct 13 10:44 images
+-rw-r--r-- 1 runner docker  1597 Oct 13 10:44 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct 13 10:44 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69877 Oct 13 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct 13 10:44 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct 13 10:44 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct 13 10:44 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct 13 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  8 10:06 data
-drwxr-xr-x 2 runner docker 4.0K Oct  8 10:06 images
--rw-r--r-- 1 runner docker 1.6K Oct  8 10:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  8 10:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  8 10:09 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  8 10:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  8 10:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  8 10:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  8 10:09 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct 13 10:44 data
+drwxr-xr-x 2 runner docker 4.0K Oct 13 10:44 images
+-rw-r--r-- 1 runner docker 1.6K Oct 13 10:44 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 13 10:44 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct 13 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct 13 10:44 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 13 10:44 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 13 10:44 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 13 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  8 10:09 .
-drwxr-xr-x 5 runner docker 4.0K Oct  8 10:09 ..
-drwxr-xr-x 2 runner docker 4.0K Oct  8 10:06 data
-drwxr-xr-x 2 runner docker 4.0K Oct  8 10:06 images
--rw-r--r-- 1 runner docker 1.6K Oct  8 10:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  8 10:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  8 10:09 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  8 10:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  8 10:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  8 10:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  8 10:09 workshop.rmarkdown</code></pre>
+drwxr-xr-x 4 runner docker 4.0K Oct 13 10:58 .
+drwxr-xr-x 5 runner docker 4.0K Oct 13 10:58 ..
+drwxr-xr-x 2 runner docker 4.0K Oct 13 10:44 data
+drwxr-xr-x 2 runner docker 4.0K Oct 13 10:44 images
+-rw-r--r-- 1 runner docker 1.6K Oct 13 10:44 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct 13 10:44 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct 13 10:58 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct 13 10:44 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 13 10:44 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 13 10:44 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 13 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>

core/week-6/overview.html

@@ -257,7 +257,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-6/study_after_workshop.html

@@ -270,7 +270,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-6/study_before_workshop.html

@@ -257,7 +257,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

core/week-6/workshop.html

@@ -278,7 +278,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

index.html

@@ -120,7 +120,7 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

omics/omics.html

@@ -269,7 +269,7 @@ <h1 class="title">Omics Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 

omics/week-3/overview.html

@@ -266,7 +266,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 
@@ -294,14 +294,13 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
 <li><p><a href="../../omics/week-3/study_before_workshop.html">Prepare</a></p>
 <ol type="i">
-<li>📖 Read how the data were generated and how they have been processed so far, install</li>
+<li>📖 Read how the data were generated and how they have been processed so far</li>
 </ol></li>
 <li><p><a href="../../omics/week-3/workshop.html">Workshop</a></p>
 <ol type="i">
 <li><p>💻 Set up a Project</p></li>
 <li><p>💻 Import data</p></li>
 <li><p>💻 Explore the distribution of values across samples/cells and across genes/species</p></li>
-<li><p>💻 Perform quality control</p></li>
 <li><p>💻 Look after future you!</p></li>
 </ol></li>
 <li><p><a href="../../omics/week-3/study_after_workshop.html">Consolidate</a></p>

omics/week-3/study_after_workshop.html

@@ -259,7 +259,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 
@@ -275,7 +275,8 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 <p>🐭 Mice</p>
 <p>🎬 Open your <code>mice-88H</code> Project. Open your <code>hspc-prog.R</code> script and, using you code working with the hspc cells as a template, repeat the analysis on the prog cells.</p>
 <p>🍂 xxxx</p>
-<p>🎬 Open your <code>xxxx-88H</code> Project. Make a new script and, using <code>xxxxxxx.R</code> as a template, repeat the analysis on xxxxxxxx</p>
+<p>Follow one of the other examples.</p>
+<!-- 🎬 Open your `xxxx-88H` Project. Make a new script and, using `xxxxxxx.R` as a template, repeat the analysis on xxxxxxxx -->
 
 
 

omics/week-3/study_before_workshop.html

@@ -357,7 +357,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">8 October, 2023</p>
+  <p class="date">13 October, 2023</p>
 </section>
 <section id="overview" class="slide level2">
 <h2>Overview</h2>

omics/week-3/workshop.html

@@ -359,7 +359,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">8 October, 2023</p>
+      <p class="date">13 October, 2023</p>
     </div>
   </div>
 
@@ -2092,7 +2092,10 @@ <h1 class="title">Workshop</h1>
 </section><section id="mice-and-future-you" class="level3"><h3 class="anchored" data-anchor-id="mice-and-future-you">🐭 Mice and future you</h3>
 <p>🎬 Create a new Project, <code>mice-88H</code>, populated with folders and your data. Make a script file called <code>hspc-prog.R</code>. This will a be commented analysis of the hspc cells vs the prog cells. At this point you will have only code for the hspc cells. You will build on this each workshop and be able to use it as a template to examine other comparisons. Copy in the appropriate code and comments from <code>workshop-1.R</code>. Edit to improve your comments where your understanding has developed since you made them. Make sure you can close down RStudio, reopen it and run your whole script again.</p>
 </section><section id="xxxx-and-future-you" class="level3"><h3 class="anchored" data-anchor-id="xxxx-and-future-you">🍂 xxxx and future you</h3>
-<p>🎬 Create a new Project, <code>xxxx-88H</code>, populated with folders and your data. Make a script file called <code>xxxx.R</code>. This will a be commented analysis of t xxxxxxxxxxxx.</p>
+<p><strong>Do one of the other two examples.</strong></p>
+<!-- 🎬 Create a new Project, `xxxx-88H`, populated with folders and your -->
+<!-- data. Make a script file called `xxxx.R`. This will a be commented -->
+<!-- analysis of t xxxxxxxxxxxx. -->
 </section></section></section><section id="finished" class="level1"><h1>🥳 Finished</h1>
 <p>Well Done!</p>
 </section><section id="independent-study-following-the-workshop" class="level1"><h1>Independent study following the workshop</h1>