Draft version for course 2.1.2 published

mkempenaar · Sep 10, 2023 · 4f04fc9 · 4f04fc9
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diff --git a/404.html b/404.html
diff --git a/a1-data_loading.html b/a1-data_loading.html
diff --git a/a2-annotation.html b/a2-annotation.html
diff --git a/a3-annotation.html b/a3-annotation.html
diff --git a/chapter-1.html b/chapter-1.html
diff --git a/chapter-2.html b/chapter-2.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Marcel Kempenaar" />
 
 
-<meta name="date" content="2023-04-24" />
+<meta name="date" content="2023-09-08" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -164,16 +164,13 @@
 </ul></li>
 <li class="chapter" data-level="1" data-path="chapter-1.html"><a href="chapter-1.html"><i class="fa fa-check"></i><b>1</b> Introduction</a>
 <ul>
-<li class="chapter" data-level="1.1" data-path="chapter-1.html"><a href="chapter-1.html#capstone-project---analysis-of-gene-expression"><i class="fa fa-check"></i><b>1.1</b> Capstone Project - Analysis of Gene Expression</a></li>
-<li class="chapter" data-level="1.2" data-path="chapter-1.html"><a href="chapter-1.html#project-deliverables"><i class="fa fa-check"></i><b>1.2</b> Project Deliverables</a></li>
-<li class="chapter" data-level="1.3" data-path="chapter-1.html"><a href="chapter-1.html#project-schedule"><i class="fa fa-check"></i><b>1.3</b> Project Schedule</a></li>
-<li class="chapter" data-level="1.4" data-path="chapter-1.html"><a href="chapter-1.html#grading"><i class="fa fa-check"></i><b>1.4</b> Grading</a></li>
-<li class="chapter" data-level="1.5" data-path="chapter-1.html"><a href="chapter-1.html#lab-journal"><i class="fa fa-check"></i><b>1.5</b> <em>Lab Journal</em></a></li>
-<li class="chapter" data-level="1.6" data-path="chapter-1.html"><a href="chapter-1.html#article"><i class="fa fa-check"></i><b>1.6</b> Article</a>
-<ul>
-<li class="chapter" data-level="1.6.1" data-path="chapter-1.html"><a href="chapter-1.html#installing-the-article-template"><i class="fa fa-check"></i><b>1.6.1</b> Installing the Article Template</a></li>
-<li class="chapter" data-level="1.6.2" data-path="chapter-1.html"><a href="chapter-1.html#using-the-template"><i class="fa fa-check"></i><b>1.6.2</b> Using the Template</a></li>
-</ul></li>
+<li class="chapter" data-level="1.1" data-path="chapter-1.html"><a href="chapter-1.html#course-changes-due-to-covid-restrictions"><i class="fa fa-check"></i><b>1.1</b> Course changes due to COVID restrictions</a></li>
+<li class="chapter" data-level="1.2" data-path="chapter-1.html"><a href="chapter-1.html#theme-7---analysis-of-gene-expression-project"><i class="fa fa-check"></i><b>1.2</b> Theme 7 - Analysis of Gene Expression Project</a></li>
+<li class="chapter" data-level="1.3" data-path="chapter-1.html"><a href="chapter-1.html#project-deliverables"><i class="fa fa-check"></i><b>1.3</b> Project Deliverables</a></li>
+<li class="chapter" data-level="1.4" data-path="chapter-1.html"><a href="chapter-1.html#project-schedule"><i class="fa fa-check"></i><b>1.4</b> Project Schedule</a></li>
+<li class="chapter" data-level="1.5" data-path="chapter-1.html"><a href="chapter-1.html#grading"><i class="fa fa-check"></i><b>1.5</b> Grading</a></li>
+<li class="chapter" data-level="1.6" data-path="chapter-1.html"><a href="chapter-1.html#project-proposal"><i class="fa fa-check"></i><b>1.6</b> Project Proposal</a></li>
+<li class="chapter" data-level="1.7" data-path="chapter-1.html"><a href="chapter-1.html#lab-journal"><i class="fa fa-check"></i><b>1.7</b> <em>Lab Journal</em></a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="chapter-2.html"><a href="chapter-2.html"><i class="fa fa-check"></i><b>2</b> Discovering Data Sets</a>
 <ul>

diff --git a/chapter-3.html b/chapter-3.html
diff --git a/chapter-4.html b/chapter-4.html
diff --git a/chapter-5.html b/chapter-5.html
diff --git a/index.html b/index.html
diff --git a/reference-keys.txt b/reference-keys.txt
@@ -15,18 +15,15 @@ fig:GEODataOverview
 fig:GEODataDownload
 tab:foo
 chapter-1
-capstone-project---analysis-of-gene-expression
+genomics
 project-deliverables
-project-schedule
-grading
+transcriptomics
+project-deliverables-1
 lab-journal
-article
-installing-the-article-template
-using-the-template
-chapter-2
-finding-public-data
-ncbi-geo
-project-proposal_ch2
+schedule
+genomics-1
+transcriptomics-1
+literature
 chapter-3
 loading-data
 ch3_example_data
@@ -67,3 +64,6 @@ manually-annotate
 annotationDBI
 using-biomart
 references
+a3-annotation
+finding-public-data
+ncbi-geo
diff --git a/search_index.json b/search_index.json