Deploying to gh-pages from @ df065c2 🚀

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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>
 

core/week-2/study_before_workshop.html

@@ -423,7 +423,7 @@
 </div>
 </div>
 
-  <p class="date">6 October, 2023</p>
+  <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>
 
@@ -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  6 15:56 data
-drwxr-xr-x 2 runner docker  4096 Oct  6 15:56 images
--rw-r--r-- 1 runner docker  1597 Oct  6 15:56 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  6 15:56 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  6 15:59 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  6 15:56 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  6 15:56 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct  6 15:56 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct  6 15:59 workshop.rmarkdown</code></pre>
+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>
 </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  6 15:56 data
-drwxr-xr-x 2 runner docker 4.0K Oct  6 15:56 images
--rw-r--r-- 1 runner docker 1.6K Oct  6 15:56 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  6 15:56 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  6 15:59 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  6 15:56 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  6 15:56 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 15:56 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 15:59 workshop.rmarkdown</code></pre>
+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>
 </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  6 15:59 .
-drwxr-xr-x 5 runner docker 4.0K Oct  6 15:58 ..
-drwxr-xr-x 2 runner docker 4.0K Oct  6 15:56 data
-drwxr-xr-x 2 runner docker 4.0K Oct  6 15:56 images
--rw-r--r-- 1 runner docker 1.6K Oct  6 15:56 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  6 15:56 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  6 15:59 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  6 15:56 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  6 15:56 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 15:56 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 15:59 workshop.rmarkdown</code></pre>
+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>
 </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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>
 

omics/omics.html

@@ -246,8 +246,8 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#content" id="toc-content" class="nav-link active" data-scroll-target="#content">Content</a>
   <ul class="collapse">
-  <li><a href="#omics-1-hello-data" id="toc-omics-1-hello-data" class="nav-link" data-scroll-target="#omics-1-hello-data">Omics 1: Hello data!</a></li>
-  <li><a href="#omics-2-statisitcal-analysis" id="toc-omics-2-statisitcal-analysis" class="nav-link" data-scroll-target="#omics-2-statisitcal-analysis">Omics 2: Statisitcal Analysis</a></li>
+  <li><a href="#omics-1-hello-data" id="toc-omics-1-hello-data" class="nav-link" data-scroll-target="#omics-1-hello-data">Omics 1: 👋 Hello data!</a></li>
+  <li><a href="#omics-2-statistical-analysis" id="toc-omics-2-statistical-analysis" class="nav-link" data-scroll-target="#omics-2-statistical-analysis">Omics 2: Statistical Analysis</a></li>
   <li><a href="#omics-3-visualising-and-interpreting" id="toc-omics-3-visualising-and-interpreting" class="nav-link" data-scroll-target="#omics-3-visualising-and-interpreting">Omics 3: Visualising and Interpreting</a></li>
   </ul></li>
   </ul>
@@ -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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>
 
@@ -282,11 +282,11 @@ <h1 class="title">Omics Data Analysis for Group Project</h1>
 <section id="content" class="level1">
 <h1>Content</h1>
 <section id="omics-1-hello-data" class="level2">
-<h2 class="anchored" data-anchor-id="omics-1-hello-data">Omics 1: Hello data!</h2>
+<h2 class="anchored" data-anchor-id="omics-1-hello-data">Omics 1: 👋 Hello data!</h2>
 <p>This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control.</p>
 </section>
-<section id="omics-2-statisitcal-analysis" class="level2">
-<h2 class="anchored" data-anchor-id="omics-2-statisitcal-analysis">Omics 2: Statisitcal Analysis</h2>
+<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>

omics/week-3/overview.html

@@ -255,7 +255,7 @@ <h2 id="toc-title">On this page</h2>
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Overview</h1>
-<p class="subtitle lead">Omics 1: Hello data!</p>
+<p class="subtitle lead">Omics 1: 👋 Hello data!</p>
 </div>
 
 
@@ -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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>
 
@@ -277,6 +277,7 @@ <h1 class="title">Overview</h1>
 </header>
 
 <p>This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control.</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>
 <p>The successful student will be able to:</p>
@@ -293,7 +294,7 @@ <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, insstall</li>
+<li>📖 Read how the data were generated and how they have been processed so far, install</li>
 </ol></li>
 <li><p><a href="../../omics/week-3/workshop.html">Workshop</a></p>
 <ol type="i">

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">6 October, 2023</p>
+      <p class="date">7 October, 2023</p>
     </div>
   </div>