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3mmaRand · Nov 3, 2023 · b5fed34 · b5fed34
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diff --git a/core/week-11/overview.html b/core/week-11/overview.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -275,7 +275,16 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+
+  <ul>
+  <li><a href="#learning-objectives" id="toc-learning-objectives" class="nav-link active" data-scroll-target="#learning-objectives">Learning objectives</a></li>
+  <li><a href="#instructions" id="toc-instructions" class="nav-link" data-scroll-target="#instructions">Instructions</a></li>
+  </ul>
+</nav>
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/core/week-11/study_after_workshop.html b/core/week-11/study_after_workshop.html
@@ -90,7 +90,7 @@
   }
 }</script><link rel="stylesheet" href="../../styles.css">
 </head>
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top"><nav class="navbar navbar-expand-lg navbar-dark "><div class="navbar-container container-fluid">
@@ -291,7 +291,13 @@
 </div>
 </nav><div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active"><h2 id="toc-title">On this page</h2>
+
+  <ul>
+<li><a href="#set-up" id="toc-set-up" class="nav-link active" data-scroll-target="#set-up">Set up</a></li>
+  </ul></nav>
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block default"><div class="quarto-title">
 <h1 class="title">Independent Study to consolidate this week</h1>

diff --git a/core/week-11/study_before_workshop.html b/core/week-11/study_before_workshop.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -275,7 +275,9 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html
@@ -463,55 +463,55 @@ <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 140
-drwxr-xr-x 2 runner docker  4096 Nov  3 15:12 data
-drwxr-xr-x 2 runner docker  4096 Nov  3 15:12 images
--rw-r--r-- 1 runner docker 26145 Nov  3 15:15 overview.html
--rw-r--r-- 1 runner docker  1597 Nov  3 15:12 overview.qmd
--rw-r--r-- 1 runner docker   184 Nov  3 15:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Nov  3 15:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Nov  3 15:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 44938 Nov  3 15:12 workshop.html
--rw-r--r-- 1 runner docker  8550 Nov  3 15:12 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Nov  3 15:15 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Nov  3 15:12 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Nov  3 15:29 data
+drwxr-xr-x 2 runner docker  4096 Nov  3 15:29 images
+-rw-r--r-- 1 runner docker 26145 Nov  3 15:32 overview.html
+-rw-r--r-- 1 runner docker  1597 Nov  3 15:29 overview.qmd
+-rw-r--r-- 1 runner docker   184 Nov  3 15:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  4807 Nov  3 15:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Nov  3 15:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 44938 Nov  3 15:29 workshop.html
+-rw-r--r-- 1 runner docker  8550 Nov  3 15:29 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Nov  3 15:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Nov  3 15:29 workshop_files</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 140K
-drwxr-xr-x 2 runner docker 4.0K Nov  3 15:12 data
-drwxr-xr-x 2 runner docker 4.0K Nov  3 15:12 images
--rw-r--r-- 1 runner docker  26K Nov  3 15:15 overview.html
--rw-r--r-- 1 runner docker 1.6K Nov  3 15:12 overview.qmd
--rw-r--r-- 1 runner docker  184 Nov  3 15:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Nov  3 15:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov  3 15:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  44K Nov  3 15:12 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov  3 15:12 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov  3 15:15 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov  3 15:12 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Nov  3 15:29 data
+drwxr-xr-x 2 runner docker 4.0K Nov  3 15:29 images
+-rw-r--r-- 1 runner docker  26K Nov  3 15:32 overview.html
+-rw-r--r-- 1 runner docker 1.6K Nov  3 15:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Nov  3 15:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Nov  3 15:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Nov  3 15:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  44K Nov  3 15:29 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Nov  3 15:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Nov  3 15:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Nov  3 15:29 workshop_files</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 148K
-drwxr-xr-x 5 runner docker 4.0K Nov  3 15:15 .
-drwxr-xr-x 6 runner docker 4.0K Nov  3 15:14 ..
-drwxr-xr-x 2 runner docker 4.0K Nov  3 15:12 data
-drwxr-xr-x 2 runner docker 4.0K Nov  3 15:12 images
--rw-r--r-- 1 runner docker  26K Nov  3 15:15 overview.html
--rw-r--r-- 1 runner docker 1.6K Nov  3 15:12 overview.qmd
--rw-r--r-- 1 runner docker  184 Nov  3 15:12 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Nov  3 15:12 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Nov  3 15:12 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  44K Nov  3 15:12 workshop.html
--rw-r--r-- 1 runner docker 8.4K Nov  3 15:12 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Nov  3 15:15 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Nov  3 15:12 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Nov  3 15:32 .
+drwxr-xr-x 6 runner docker 4.0K Nov  3 15:31 ..
+drwxr-xr-x 2 runner docker 4.0K Nov  3 15:29 data
+drwxr-xr-x 2 runner docker 4.0K Nov  3 15:29 images
+-rw-r--r-- 1 runner docker  26K Nov  3 15:32 overview.html
+-rw-r--r-- 1 runner docker 1.6K Nov  3 15:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Nov  3 15:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Nov  3 15:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Nov  3 15:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  44K Nov  3 15:29 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Nov  3 15:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Nov  3 15:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Nov  3 15:29 workshop_files</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>

diff --git a/core/week-6/overview.html b/core/week-6/overview.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -275,7 +275,15 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+
+  <ul>
+  <li><a href="#instructions" id="toc-instructions" class="nav-link active" data-scroll-target="#instructions">Instructions</a></li>
+  </ul>
+</nav>
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/core/week-6/study_after_workshop.html b/core/week-6/study_after_workshop.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -275,7 +275,9 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/core/week-6/study_before_workshop.html b/core/week-6/study_before_workshop.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -275,7 +275,9 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/omics/week-5/figures/prog-hspc-volcano.png b/omics/week-5/figures/prog-hspc-volcano.png
diff --git a/omics/week-5/workshop.html b/omics/week-5/workshop.html
diff --git a/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png b/omics/week-5/workshop_files/figure-html/unnamed-chunk-33-1.png
diff --git a/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png b/omics/week-5/workshop_files/figure-html/unnamed-chunk-65-1.png