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SydneyBioX · Oct 24, 2023 · 69ba619 · 69ba619
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-68fff12f
+5e7c17d7
diff --git a/search.json b/search.json
@@ -151,14 +151,21 @@
     "href": "workshops.html",
     "title": "Problem-focused Workshops",
     "section": "",
-    "text": "The Sydney Precision Data Science Centre runs several workshops that teach attendees to deal with the complexities of single cell data. These workshops target a specific challenge related to single cell data and show attendees how to address it while highlighting the nuances in each step of the process."
+    "text": "The Sydney Precision Data Science Centre has developed a series of living workshops for building data stories, using Single-cell data integrative analysis (scdney). scdney is a wrapper package with a collection of single-cell analysis R packages incorporating data integration, cell type annotation, higher order testing and more. Through these workshops, we not only showcase current solutions, but also highlight critical thinking points. In particular, we highlight the Thinking Process Template that provides a structured framework for the decision-making process behind such single-cell analyses. Furthermore, our workshop will incorporate dynamic contributions from the community in a collaborative learning approach, thus the term ‘living’. For more information on the Thinking Process Template, please see our F1000 publication (https://f1000research.com/articles/12-261)"
   },
   {
     "objectID": "workshops.html#fondation-workshop",
     "href": "workshops.html#fondation-workshop",
     "title": "Problem-focused Workshops",
     "section": "Fondation workshop",
-    "text": "Fondation workshop\nThe foundation workshop focuses on the basic aspect of navigating and visualising single-cell data. Additionally it covers aspects such as:\n\nQuality control\nNormalisation\nBatch correction\nCell-type annotation with marker genes\nCell-type clustering\n\n\nAdvanced extension\nAdditionally, the foundation workshop can be extended to include advanced topics such as:\n\nMerging datasets\nBatch effect quantification and visualisation\nJoint cell-type annotation\nCell-type annotation quality control\nMarker and pathway analysis\nGene regulatory network analysis"
+    "text": "Fondation workshop\nThe foundation workshop focuses on the basic aspect of navigating and visualising single-cell data. Additionally it covers aspects such as:\n\nQuality control\nNormalisation\nBatch correction\nCell-type annotation with marker genes\nCell-type clustering"
+  },
+  {
+    "objectID": "workshops.html#advanced-foundation-extension-workshop",
+    "href": "workshops.html#advanced-foundation-extension-workshop",
+    "title": "Problem-focused Workshops",
+    "section": "Advanced foundation extension workshop",
+    "text": "Advanced foundation extension workshop\nAdditionally, the foundation workshop can be extended to include advanced topics such as:\n\nMerging datasets\nBatch effect quantification and visualisation\nJoint cell-type annotation\nCell-type annotation quality control\nMarker and pathway analysis\nGene regulatory network analysis"
   },
   {
     "objectID": "workshops.html#advanced-cell-phenotyping",

diff --git a/sitemap.xml b/sitemap.xml
@@ -2,22 +2,22 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://SydneyBioX.github.io/scdney_devel/about.html</loc>
-    <lastmod>2023-10-23T01:20:30.335Z</lastmod>
+    <lastmod>2023-10-24T23:50:08.376Z</lastmod>
   </url>
   <url>
     <loc>https://SydneyBioX.github.io/scdney_devel/software.html</loc>
-    <lastmod>2023-10-23T01:20:29.829Z</lastmod>
+    <lastmod>2023-10-24T23:50:07.822Z</lastmod>
   </url>
   <url>
     <loc>https://SydneyBioX.github.io/scdney_devel/index.html</loc>
-    <lastmod>2023-10-23T01:20:28.562Z</lastmod>
+    <lastmod>2023-10-24T23:50:06.312Z</lastmod>
   </url>
   <url>
     <loc>https://SydneyBioX.github.io/scdney_devel/workshops.html</loc>
-    <lastmod>2023-10-23T01:20:28.745Z</lastmod>
+    <lastmod>2023-10-24T23:50:06.519Z</lastmod>
   </url>
   <url>
     <loc>https://SydneyBioX.github.io/scdney_devel/Publications.html</loc>
-    <lastmod>2023-10-23T01:20:30.182Z</lastmod>
+    <lastmod>2023-10-24T23:50:08.192Z</lastmod>
   </url>
 </urlset>
diff --git a/workshops.html b/workshops.html
@@ -120,10 +120,8 @@
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#fondation-workshop" id="toc-fondation-workshop" class="nav-link active" data-scroll-target="#fondation-workshop">Fondation workshop</a>
-  <ul class="collapse">
-  <li><a href="#advanced-extension" id="toc-advanced-extension" class="nav-link" data-scroll-target="#advanced-extension">Advanced extension</a></li>
-  </ul></li>
+  <li><a href="#fondation-workshop" id="toc-fondation-workshop" class="nav-link active" data-scroll-target="#fondation-workshop">Fondation workshop</a></li>
+  <li><a href="#advanced-foundation-extension-workshop" id="toc-advanced-foundation-extension-workshop" class="nav-link" data-scroll-target="#advanced-foundation-extension-workshop">Advanced foundation extension workshop</a></li>
   <li><a href="#advanced-cell-phenotyping" id="toc-advanced-cell-phenotyping" class="nav-link" data-scroll-target="#advanced-cell-phenotyping">Advanced cell phenotyping</a></li>
   <li><a href="#disease-outcome-classification-in-single-cell-data" id="toc-disease-outcome-classification-in-single-cell-data" class="nav-link" data-scroll-target="#disease-outcome-classification-in-single-cell-data">Disease Outcome Classification in Single Cell Data</a></li>
   </ul>
@@ -149,7 +147,7 @@ <h1 class="title">Problem-focused Workshops</h1>
 
 </header>
 
-<p>The Sydney Precision Data Science Centre runs several workshops that teach attendees to deal with the complexities of single cell data. These workshops target a specific challenge related to single cell data and show attendees how to address it while highlighting the nuances in each step of the process.</p>
+<p>The Sydney Precision Data Science Centre has developed a series of living workshops for building data stories, using Single-cell data integrative analysis (scdney). scdney is a wrapper package with a collection of single-cell analysis R packages incorporating data integration, cell type annotation, higher order testing and more. Through these workshops, we not only showcase current solutions, but also highlight critical thinking points. In particular, we highlight the Thinking Process Template that provides a structured framework for the decision-making process behind such single-cell analyses. Furthermore, our workshop will incorporate dynamic contributions from the community in a collaborative learning approach, thus the term ‘living’. For more information on the Thinking Process Template, please see our F1000 publication (https://f1000research.com/articles/12-261)</p>
 <section id="fondation-workshop" class="level2">
 <h2 class="anchored" data-anchor-id="fondation-workshop">Fondation workshop</h2>
 <p>The foundation workshop focuses on the basic aspect of navigating and visualising single-cell data. Additionally it covers aspects such as:</p>
@@ -160,8 +158,9 @@ <h2 class="anchored" data-anchor-id="fondation-workshop">Fondation workshop</h2>
 <li>Cell-type annotation with marker genes</li>
 <li>Cell-type clustering</li>
 </ul>
-<section id="advanced-extension" class="level3">
-<h3 class="anchored" data-anchor-id="advanced-extension">Advanced extension</h3>
+</section>
+<section id="advanced-foundation-extension-workshop" class="level2">
+<h2 class="anchored" data-anchor-id="advanced-foundation-extension-workshop">Advanced foundation extension workshop</h2>
 <p>Additionally, the foundation workshop can be extended to include advanced topics such as:</p>
 <ul>
 <li>Merging datasets</li>
@@ -172,9 +171,8 @@ <h3 class="anchored" data-anchor-id="advanced-extension">Advanced extension</h3>
 <li>Gene regulatory network analysis</li>
 </ul>
 </section>
-</section>
 <section id="advanced-cell-phenotyping" class="level2">
-<h2 class="anchored" data-anchor-id="advanced-cell-phenotyping">Advanced cell phenotyping</h2>
+<h2 class="anchored" data-anchor-id="advanced-cell-phenotyping"><a href="https://sydneybiox.github.io/scdneyAdvancedPhenotyping/articles/advanced_phenotyping.html">Advanced cell phenotyping</a></h2>
 <p>The advanced cell phenotyping workshop guides attendees through the process for annotating cells beyond cell-type.</p>
 <ul>
 <li>Trajectory analysis
@@ -189,7 +187,7 @@ <h2 class="anchored" data-anchor-id="advanced-cell-phenotyping">Advanced cell ph
 </ul>
 </section>
 <section id="disease-outcome-classification-in-single-cell-data" class="level2">
-<h2 class="anchored" data-anchor-id="disease-outcome-classification-in-single-cell-data">Disease Outcome Classification in Single Cell Data</h2>
+<h2 class="anchored" data-anchor-id="disease-outcome-classification-in-single-cell-data"><a href="https://sydneybiox.github.io/scdneyDiseasePrediction/articles/disease_outcome_classification_schulte.html">Disease Outcome Classification in Single Cell Data</a></h2>
 <p>The disease outcome classification guides attendee through using single cell data to classify disease outcome.</p>
 <ul>
 <li>Generating features from single cell data</li>