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sib-swiss · Aug 28, 2024 · b78b2ac · b78b2ac
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-2b7aa918
+6cf13ba9
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/2_quality_control_files/figure-html/unnamed-chunk-10-1.png b/2_quality_control_files/figure-html/unnamed-chunk-10-1.png
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diff --git a/3_normalization_scaling.html b/3_normalization_scaling.html
diff --git a/3_normalization_scaling_files/figure-html/unnamed-chunk-5-1.png b/3_normalization_scaling_files/figure-html/unnamed-chunk-5-1.png
diff --git a/3_normalization_scaling_files/figure-html/unnamed-chunk-6-1.png b/3_normalization_scaling_files/figure-html/unnamed-chunk-6-1.png
diff --git a/4_integration_clustering.html b/4_integration_clustering.html
diff --git a/4_integration_clustering_files/figure-html/unnamed-chunk-12-1.png b/4_integration_clustering_files/figure-html/unnamed-chunk-12-1.png
diff --git a/4_integration_clustering_files/figure-html/unnamed-chunk-15-1.png b/4_integration_clustering_files/figure-html/unnamed-chunk-15-1.png
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diff --git a/4_integration_clustering_files/figure-html/unnamed-chunk-5-1.png b/4_integration_clustering_files/figure-html/unnamed-chunk-5-1.png
diff --git a/4_integration_clustering_files/figure-html/unnamed-chunk-6-1.png b/4_integration_clustering_files/figure-html/unnamed-chunk-6-1.png
diff --git a/4_integration_clustering_files/figure-html/unnamed-chunk-9-1.png b/4_integration_clustering_files/figure-html/unnamed-chunk-9-1.png
diff --git a/5_marker_gene_identification.html b/5_marker_gene_identification.html
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-10-1.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-10-1.png
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-5-1.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-5-1.png
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-6-1.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-6-1.png
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-6-2.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-6-2.png
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-7-1.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-7-1.png
diff --git a/5_marker_gene_identification_files/figure-html/unnamed-chunk-7-2.png b/5_marker_gene_identification_files/figure-html/unnamed-chunk-7-2.png
diff --git a/course_schedule.html b/course_schedule.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Spatial transcriptomics - Course schedule</title>
+<title>Course schedule – Spatial transcriptomics</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -68,6 +68,21 @@
   }
 }</script>
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Sans+Pro">
+<!-- Matomo -->
+<script>
+  var _paq = window._paq = window._paq || [];
+  /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+  _paq.push(['trackPageView']);
+  _paq.push(['enableLinkTracking']);
+  (function() {
+    var u="https://matomo.sib.swiss/";
+    _paq.push(['setTrackerUrl', u+'matomo.php']);
+    _paq.push(['setSiteId', '220']);
+    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+    g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
+  })();
+</script>
+<!-- End Matomo Code -->
 
 
 </head>
@@ -84,7 +99,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -102,7 +117,7 @@
 <span class="menu-text">Course schedule</span></a>
   </li>  
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Course material</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-course-material">    
@@ -137,17 +152,17 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-          <div class="quarto-navbar-tools">
+            <div class="quarto-navbar-tools">
 </div>
       </div> <!-- /container-fluid -->
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item">Course schedule</li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -164,7 +179,7 @@
 </nav>
 <div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
 
     </div>
 <!-- main -->
@@ -306,18 +321,7 @@ <h1 class="title">Course schedule</h1>
     }
     return false;
   }
-  const clipboard = new window.ClipboardJS('.code-copy-button', {
-    text: function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-    }
-  });
-  clipboard.on('success', function(e) {
+  const onCopySuccess = function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -349,15 +353,37 @@ <h1 class="title">Course schedule</h1>
     }, 1000);
     // clear code selection
     e.clearSelection();
+  }
+  const getTextToCopy = function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+    text: getTextToCopy
   });
+  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')
+    });
+    clipboardModal.on('success', onCopySuccess);
+  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/sib-swiss\.github\.io\/spatial-transcriptomics-training\/");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {

diff --git a/index.html b/index.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Spatial transcriptomics - SIB Days tutorial: Analysis of spatial transcriptomics data</title>
+<title>SIB Days tutorial: Analysis of spatial transcriptomics data – Spatial transcriptomics</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -68,6 +68,21 @@
   }
 }</script>
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Sans+Pro">
+<!-- Matomo -->
+<script>
+  var _paq = window._paq = window._paq || [];
+  /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+  _paq.push(['trackPageView']);
+  _paq.push(['enableLinkTracking']);
+  (function() {
+    var u="https://matomo.sib.swiss/";
+    _paq.push(['setTrackerUrl', u+'matomo.php']);
+    _paq.push(['setSiteId', '220']);
+    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+    g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
+  })();
+</script>
+<!-- End Matomo Code -->
 
 
 </head>
@@ -84,7 +99,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -102,7 +117,7 @@
 <span class="menu-text">Course schedule</span></a>
   </li>  
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Course material</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-course-material">    
@@ -137,17 +152,17 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-          <div class="quarto-navbar-tools">
+            <div class="quarto-navbar-tools">
 </div>
       </div> <!-- /container-fluid -->
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item">SIB Days tutorial: Analysis of spatial transcriptomics data</li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -278,18 +293,7 @@ <h3 class="anchored" data-anchor-id="exercises">Exercises</h3>
     }
     return false;
   }
-  const clipboard = new window.ClipboardJS('.code-copy-button', {
-    text: function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-    }
-  });
-  clipboard.on('success', function(e) {
+  const onCopySuccess = function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -321,15 +325,37 @@ <h3 class="anchored" data-anchor-id="exercises">Exercises</h3>
     }, 1000);
     // clear code selection
     e.clearSelection();
+  }
+  const getTextToCopy = function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+    text: getTextToCopy
   });
+  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')
+    });
+    clipboardModal.on('success', onCopySuccess);
+  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/sib-swiss\.github\.io\/spatial-transcriptomics-training\/");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {