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rnabioco · Jul 24, 2024 · d9b4513 · d9b4513
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-b9479532
+60eeab03
diff --git a/atlases.html b/atlases.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-1.4.550">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>LNSC Browser - Atlases</title>
+<title>Atlases – LNSC Browser</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -100,7 +100,7 @@
   })
   </script>
 
-  <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
+  <script src="https://cdnjs.cloudflare.com/polyfill/v3/polyfill.min.js?features=es6"></script>
   <script src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js" type="text/javascript"></script>
 
 <script type="text/javascript">
@@ -138,13 +138,13 @@
   <header id="quarto-header" class="headroom fixed-top">
   <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"><a href="./atlases.html">Atlases</a></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>
-      <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
+      <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
         <i class="bi bi-search"></i>
       </button>
     </div>
@@ -229,10 +229,12 @@ <h1 class="title">Atlases</h1>
 
 <div class="quarto-listing quarto-listing-container-grid" id="listing-listing">
 <div class="list grid quarto-listing-cols-3">
-<div class="g-col-1" data-index="0" data-categories="Project-1,Project-2,Core-C,Core-D,2024" data-listing-date-sort="1704758400000" data-listing-file-modified-sort="1708928032146" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="178">
+<div class="g-col-1" data-index="0" data-categories="Project-1,Project-2,Core-C,Core-D,2024" data-listing-date-sort="1704758400000" data-listing-file-modified-sort="1721840612974" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="178">
 <a href="./atlases/2024-lucas-38194268/index.html" class="quarto-grid-link">
 </a><div class="quarto-grid-item card h-100 card-left"><a href="./atlases/2024-lucas-38194268/index.html" class="quarto-grid-link">
-<div class="listing-item-img-placeholder card-img-top" style="height: 150px;">&nbsp;</div>
+<p class="card-img-top">
+<img loading="lazy" src="./images/2024-lucas-38194268.jpg" class="thumbnail-image card-img" style="height: 150px;">
+</p>
 </a><div class="card-body post-contents"><a href="./atlases/2024-lucas-38194268/index.html" class="quarto-grid-link">
 <h5 class="no-anchor card-title listing-title">
 Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
@@ -266,11 +268,11 @@ <h5 class="no-anchor card-title listing-title">
 </div>
 
 </div>
-<div class="g-col-1" data-index="1" data-categories="Project-1,Project-2,Core-C,Core-D,2021" data-listing-date-sort="1636934400000" data-listing-file-modified-sort="1708928032146" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="203">
+<div class="g-col-1" data-index="1" data-categories="Project-1,Project-2,Core-C,Core-D,2021" data-listing-date-sort="1636934400000" data-listing-file-modified-sort="1721840612974" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="203">
 <a href="./atlases/2021-carpentier-34618370/index.html" class="quarto-grid-link">
 </a><div class="quarto-grid-item card h-100 card-left"><a href="./atlases/2021-carpentier-34618370/index.html" class="quarto-grid-link">
 <p class="card-img-top">
-<img src="./images/2021-carpentier-34618370.jpg" class="thumbnail-image card-img" style="height: 150px;">
+<img loading="lazy" src="./images/2021-carpentier-34618370.jpg" class="thumbnail-image card-img" style="height: 150px;">
 </p>
 </a><div class="card-body post-contents"><a href="./atlases/2021-carpentier-34618370/index.html" class="quarto-grid-link">
 <h5 class="no-anchor card-title listing-title">
@@ -305,11 +307,11 @@ <h5 class="no-anchor card-title listing-title">
 </div>
 
 </div>
-<div class="g-col-1" data-index="2" data-categories="Project-2,Core-C,Core-D,2021" data-listing-date-sort="1618185600000" data-listing-file-modified-sort="1708928032146" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="169">
+<div class="g-col-1" data-index="2" data-categories="Project-2,Core-C,Core-D,2021" data-listing-date-sort="1618185600000" data-listing-file-modified-sort="1721840612974" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="169">
 <a href="./atlases/2021-walsh-33843587/index.html" class="quarto-grid-link">
 </a><div class="quarto-grid-item card h-100 card-left"><a href="./atlases/2021-walsh-33843587/index.html" class="quarto-grid-link">
 <p class="card-img-top">
-<img src="./images/2021-walsh-33843587.jpg" class="thumbnail-image card-img" style="height: 150px;">
+<img loading="lazy" src="./images/2021-walsh-33843587.jpg" class="thumbnail-image card-img" style="height: 150px;">
 </p>
 </a><div class="card-body post-contents"><a href="./atlases/2021-walsh-33843587/index.html" class="quarto-grid-link">
 <h5 class="no-anchor card-title listing-title">
@@ -525,18 +527,7 @@ <h5 class="no-anchor card-title listing-title">
     }
     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
@@ -568,18 +559,45 @@ <h5 class="no-anchor card-title listing-title">
     }, 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:\/\/lnsc-cell-browser\.org");
     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)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
           // target, if specified
           link.setAttribute("target", "_blank");
           if (link.getAttribute("rel") === null) {
@@ -621,7 +639,11 @@ <h5 class="no-anchor card-title listing-title">
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');

diff --git a/atlases/2021-carpentier-34618370/index.html b/atlases/2021-carpentier-34618370/index.html
@@ -2,13 +2,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.550">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="dcterms.date" content="2021-11-15">
 
-<title>LNSC Browser - MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination</title>
+<title>MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination – LNSC Browser</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -78,15 +78,15 @@
   <header id="quarto-header" class="headroom fixed-top">
   <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">
       LNSC Browser
       </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>
-      <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
+      <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
         <i class="bi bi-search"></i>
       </button>
     </div>
@@ -142,7 +142,7 @@
 <!-- margin-sidebar -->
 
 <!-- main -->
-<div class="quarto-about-jolla content">
+<div class="quarto-about-jolla">
   <img src="/images/2021-carpentier-34618370.jpg" class="about-image
   round " style="height: 15em; width: 15em;">
  <header id="title-block-header" class="quarto-title-block default">
@@ -363,18 +363,7 @@ <h1 class="title">MARCO+ lymphatic endothelial cells sequester arthritogenic alp
     }
     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
@@ -406,18 +395,45 @@ <h1 class="title">MARCO+ lymphatic endothelial cells sequester arthritogenic alp
     }, 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:\/\/lnsc-cell-browser\.org");
     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)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
           // target, if specified
           link.setAttribute("target", "_blank");
           if (link.getAttribute("rel") === null) {
@@ -459,7 +475,11 @@ <h1 class="title">MARCO+ lymphatic endothelial cells sequester arthritogenic alp
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');