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sib-swiss · Dec 1, 2024 · bdb5646 · bdb5646
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Showing 15 changed files with 154 additions and 175 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-393b9371
+bde7893f
diff --git a/1_setup.html b/1_setup.html
diff --git a/2_quality_control.html b/2_quality_control.html
diff --git a/3_normalization_scaling.html b/3_normalization_scaling.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.57">
+<meta name="generator" content="quarto-1.6.39">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -70,10 +70,10 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-4d7b8eec1c60cc33e64fe606aab9e7fe.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -471,8 +471,6 @@ <h2 class="anchored" data-anchor-id="normalization-and-scaling-with-sctransform"
   });
   clipboard.on('success', onCopySuccess);
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -583,7 +581,6 @@ <h2 class="anchored" data-anchor-id="normalization-and-scaling-with-sctransform"
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
-      // TODO in 1.5, we should make sure this works without a callout special case
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {

diff --git a/4_integration_clustering.html b/4_integration_clustering.html
diff --git a/5_marker_gene_identification.html b/5_marker_gene_identification.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.57">
+<meta name="generator" content="quarto-1.6.39">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -70,10 +70,10 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-4d7b8eec1c60cc33e64fe606aab9e7fe.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -658,8 +658,6 @@ <h2 class="anchored" data-anchor-id="bonus-exercise-spatially-variable-features"
   });
   clipboard.on('success', onCopySuccess);
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -770,7 +768,6 @@ <h2 class="anchored" data-anchor-id="bonus-exercise-spatially-variable-features"
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
-      // TODO in 1.5, we should make sure this works without a callout special case
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {

diff --git a/course_schedule.html b/course_schedule.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.57">
+<meta name="generator" content="quarto-1.6.39">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -36,10 +36,10 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-4d7b8eec1c60cc33e64fe606aab9e7fe.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -368,8 +368,6 @@ <h1 class="title">Course schedule</h1>
   });
   clipboard.on('success', onCopySuccess);
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -480,7 +478,6 @@ <h1 class="title">Course schedule</h1>
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
-      // TODO in 1.5, we should make sure this works without a callout special case
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {

diff --git a/index.html b/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.57">
+<meta name="generator" content="quarto-1.6.39">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -36,10 +36,10 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-4d7b8eec1c60cc33e64fe606aab9e7fe.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -340,8 +340,6 @@ <h3 class="anchored" data-anchor-id="exercises">Exercises</h3>
   });
   clipboard.on('success', onCopySuccess);
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -452,7 +450,6 @@ <h3 class="anchored" data-anchor-id="exercises">Exercises</h3>
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
-      // TODO in 1.5, we should make sure this works without a callout special case
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {

diff --git a/precourse_preparations.html b/precourse_preparations.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.57">
+<meta name="generator" content="quarto-1.6.39">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -36,10 +36,10 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-4d7b8eec1c60cc33e64fe606aab9e7fe.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -297,8 +297,6 @@ <h1 class="title">Precourse preparations</h1>
   });
   clipboard.on('success', onCopySuccess);
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
-    // For code content inside modals, clipBoardJS needs to be initialized with a container option
-    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -409,7 +407,6 @@ <h1 class="title">Precourse preparations</h1>
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
-      // TODO in 1.5, we should make sure this works without a callout special case
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {