Merge branch 'master' of https://github.com/BaderLab/CBW_Pathways_2024

BaderLab · Jun 25, 2024 · 2f0bb6b · 2f0bb6b
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diff --git a/3.0-Module3_Visualizing_ORA_analysis.Rmd b/3.0-Module3_Visualizing_ORA_analysis.Rmd
@@ -2,18 +2,26 @@
 
  *<font color="#827e9c">Ruth Isserlin</font>*
 
- [Lecture part 1](./lectures/Pathways_2024_Module3-part1-Cytoscape-RI.pdf)
-
- [Lecture part 2](./lectures/Pathways_2024_Module3-part2-EM-RI.pdf) 
+ **Module 3 Cytoscape** 
 
-**Module 3 Lab**
+ [Cytoscape - Lecture](./lectures/Pathways_2024_Module3-part1-Cytoscape-RI.pdf)
 
- *<font color="#827e9c">Ruth Isserlin</font>*  
+ **Module 3 Cytoscape Lab**
 
-[Introduction to practical Lab](./lectures/Pathways_2024_Module3_lab_introduction_RI.pdf)
+[Introduction to practical Cytoscape Lab (slides)](./lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf)
 
 [Lab practical Cytoscape Primer](#cytoscape_mod3) 
 
+---- 
+
+ **Module 3 Enrichment Map** 
+
+[Enrichment Map Lecture](./lectures/Pathways_2024_Module3-part2-EM-RI.pdf) 
+
+ **Module 3 Enrichment Map Lab**
+
+[Introduction to practical EM Lab (slides)](./lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf)
+
 [Lab practical part 1 (g:Profiler)](#gprofiler_mod3)   
 
 [Lab practical part 2 (GSEA)](#gseq_mod3)  
diff --git a/7.1-Module6_Integrated_Assignment.Rmd b/7.1-Module6_Integrated_Assignment.Rmd
@@ -185,7 +185,7 @@ Note: you may get slightly different results as 100 permutations is not enough t
    * Click on 'Submit'.
    * Observe the iRegulon results in the Results Panel.
 
-<img src="./IntegratedAssignment/images/IA-iregulon2.png" alt="IA-iregulon2.png" width="400" />
+<img src="./IntegratedAssignment/images/IA_iregulon2.png" alt="IA-iregulon2.png" width="400" />
 
 <img src="./IntegratedAssignment/images/IA-iregulon3.png" alt="IA-iregulon3.png" width="750" />
 

diff --git a/docs/IntegratedAssignment/images/IA_iregulon2.png b/docs/IntegratedAssignment/images/IA_iregulon2.png
diff --git a/docs/gsea-lab.html b/docs/gsea-lab.html
@@ -733,7 +733,7 @@ <h3>Step1.<a href="gsea-lab.html#step1." class="anchor-section" aria-label="Anch
 </p>
 <p>
 Follow instructions specified on download page: * <img
-src="./Module2/gsea/images/gsea_troubleshooting.png" />
+src="Module2/gsea/images/gsea_troubleshooting.png" />
 </p>
 <ul>
 <li>

diff --git a/docs/integrated_assignment.html b/docs/integrated_assignment.html
@@ -784,7 +784,7 @@ <h2>PART 6: iRegulon<a href="integrated_assignment.html#part-6-iregulon" class="
 <li>Click on ‘Submit’.</li>
 <li>Observe the iRegulon results in the Results Panel.</li>
 </ul>
-<p><img src="./IntegratedAssignment/images/IA-iregulon2.png" alt="IA-iregulon2.png" width="400" /></p>
+<p><img src="IntegratedAssignment/images/IA_iregulon2.png" alt="IA-iregulon2.png" width="400" /></p>
 <p><img src="IntegratedAssignment/images/IA-iregulon3.png" alt="IA-iregulon3.png" width="750" /></p>
 <ol start="4" style="list-style-type: decimal">
 <li>Add TCF12 and AVEN to the network.</li>

diff --git a/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf b/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf
diff --git a/...ways_2024_Module3_lab_introduction_RI.pdf → ...s_2024_Module3_EM_lab_introduction_RI.pdf b/...ways_2024_Module3_lab_introduction_RI.pdf → ...s_2024_Module3_EM_lab_introduction_RI.pdf
diff --git a/docs/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf b/docs/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf
diff --git a/docs/module-2-finding-over-represented-pathways-veronique-voisin.html b/docs/module-2-finding-over-represented-pathways-veronique-voisin.html
diff --git a/docs/module-3-network-visualization-and-analysis-with-cytoscape.html b/docs/module-3-network-visualization-and-analysis-with-cytoscape.html
@@ -623,12 +623,16 @@ <h1>
 <div id="module-3-network-visualization-and-analysis-with-cytoscape" class="section level1 hasAnchor">
 <h1>Module 3: Network Visualization and Analysis with Cytoscape<a href="module-3-network-visualization-and-analysis-with-cytoscape.html#module-3-network-visualization-and-analysis-with-cytoscape" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p><em><font color="#827e9c">Ruth Isserlin</font></em></p>
-<p><a href="./lectures/Pathways_2024_Module3-part1-Cytoscape-RI.pdf">Lecture part 1</a></p>
-<p><a href="./lectures/Pathways_2024_Module3-part2-EM-RI.pdf">Lecture part 2</a></p>
-<p><strong>Module 3 Lab</strong></p>
-<p><em><font color="#827e9c">Ruth Isserlin</font></em></p>
-<p><a href="./lectures/Pathways_2024_Module3_lab_introduction_RI.pdf">Introduction to practical Lab</a></p>
+<p><strong>Module 3 Cytoscape</strong></p>
+<p><a href="./lectures/Pathways_2024_Module3-part1-Cytoscape-RI.pdf">Cytoscape - Lecture</a></p>
+<p><strong>Module 3 Cytoscape Lab</strong></p>
+<p><a href="./lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf">Introduction to practical Cytoscape Lab (slides)</a></p>
 <p><a href="cytoscape_mod3.html#cytoscape_mod3">Lab practical Cytoscape Primer</a></p>
+<hr />
+<p><strong>Module 3 Enrichment Map</strong></p>
+<p><a href="./lectures/Pathways_2024_Module3-part2-EM-RI.pdf">Enrichment Map Lecture</a></p>
+<p><strong>Module 3 Enrichment Map Lab</strong></p>
+<p><a href="./lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf">Introduction to practical EM Lab (slides)</a></p>
 <p><a href="gprofiler_mod3.html#gprofiler_mod3">Lab practical part 1 (g:Profiler)</a></p>
 <p><a href="#gseq_mod3">Lab practical part 2 (GSEA)</a></p>
-Original file line number
+Diff line change
@@ Expand Up @@
     </p>
     <p>
     Follow instructions specified on download page: * <img
-    src="./Module2/gsea/images/gsea_troubleshooting.png" />
+    src="Module2/gsea/images/gsea_troubleshooting.png" />
     </p>
     <ul>
     <li>
@@ Expand Down @@