lecture

BaderLab · Jun 25, 2024 · b03644a · b03644a
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diff --git a/2.0-Module2_Finding_Overrep_Pathways.Rmd b/2.0-Module2_Finding_Overrep_Pathways.Rmd
@@ -2,7 +2,7 @@
 
  *<font color="#827e9c">Veronique Voisin and Ruth Isserlin</font>*
 
-  [Lecture](./lectures/Pathways_2023_Module2_ORA_VV.pdf) 
+  [Lecture](./lectures/Pathways_2024_Module2_ORA_VV.pdf) 
 
   [Introduction to practical lab](./lectures/Pathways_2024_Module2_lab_introduction_RI.pdf)  
 

diff --git a/6.0-Module6_Cell_Cell_Communication.Rmd b/6.0-Module6_Cell_Cell_Communication.Rmd
@@ -6,7 +6,7 @@
 
 Gregory Schwartz
 
-[Lecture](TOADD)  
+[Lecture](./lectures/Pathways_2024_module6_Schwartz.pdf)
 
 
 ## scRNA lab praticals

diff --git a/7.0-Module6_Review_of_the_tools.Rmd b/7.0-Module6_Review_of_the_tools.Rmd
@@ -3,14 +3,14 @@
  *<font color="#827e9c">By Veronique Voisin, Chaitra Sarathy and Ruth Isserlin</font>*
 
 ## Final slides
-[Lecture](./lectures/Pathways_2023_finalslides.pdf)  
+[Lecture](./lectures/Pathways_2024_finalslides.pdf)  
 
 
 ## scRNA lab praticals
 
 [scRNA-lab1_PBMC](#scRNA-lab1)
 
- - This lab starts from scRNA data from peripheral blood mononuclear cells. 
+ - This lab starts from scRNA data from peripheral blood mononuclear cells.  
 
  - The cells from similar cell types were grouped into clusters. 
 

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/index.html b/docs/index.html
@@ -623,7 +623,7 @@ <h1>
 <div id="header">
 <h1 class="title">Pathway and Network Analysis of -Omics Data ( June 2024 )</h1>
 <p class="author"><em>Gary Bader, Ruth Isserlin, Chaitra Sarathy, Veronique Voisin</em></p>
-<p class="date"><em>last modified 2024-06-24</em></p>
+<p class="date"><em>last modified 2024-06-25</em></p>
 </div>
 <div id="canadian-bioinformatics-workshops" class="section level1 hasAnchor">
 <h1>Canadian Bioinformatics Workshops<a href="index.html#canadian-bioinformatics-workshops" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/docs/lectures/Pathways_2024_Module2_ORA_VV.pdf b/docs/lectures/Pathways_2024_Module2_ORA_VV.pdf
diff --git a/docs/lectures/Pathways_2024_finalslides.pdf b/docs/lectures/Pathways_2024_finalslides.pdf
diff --git a/docs/lectures/Pathways_2024_module6_Schwartz.pdf b/docs/lectures/Pathways_2024_module6_Schwartz.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-6-cell-cell-communication.html b/docs/module-6-cell-cell-communication.html
@@ -626,7 +626,7 @@ <h1>Module 6: Cell Cell Communication<a href="module-6-cell-cell-communication.h
 <div id="module-6-lecture-cell-cell-communication." class="section level2 hasAnchor">
 <h2>Module 6 lecture : Cell-Cell Communication.<a href="module-6-cell-cell-communication.html#module-6-lecture-cell-cell-communication." class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Gregory Schwartz</p>
-<p><a href="TOADD">Lecture</a></p>
+<p><a href="./lectures/Pathways_2024_module6_Schwartz.pdf">Lecture</a></p>
 </div>
 <div id="scrna-lab-praticals" class="section level2 hasAnchor">
 <h2>scRNA lab praticals<a href="module-6-cell-cell-communication.html#scrna-lab-praticals" class="anchor-section" aria-label="Anchor link to header"></a></h2>

diff --git a/docs/module-7-review-of-the-tools.html b/docs/module-7-review-of-the-tools.html
@@ -625,7 +625,7 @@ <h1>Module 7: Review of the tools<a href="module-7-review-of-the-tools.html#modu
 <p><em><font color="#827e9c">By Veronique Voisin, Chaitra Sarathy and Ruth Isserlin</font></em></p>
 <div id="final-slides" class="section level2 hasAnchor">
 <h2>Final slides<a href="module-7-review-of-the-tools.html#final-slides" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<p><a href="./lectures/Pathways_2023_finalslides.pdf">Lecture</a></p>
+<p><a href="./lectures/Pathways_2024_finalslides.pdf">Lecture</a></p>
 </div>
 <div id="scrna-lab-praticals-1" class="section level2 hasAnchor">
 <h2>scRNA lab praticals<a href="module-7-review-of-the-tools.html#scrna-lab-praticals-1" class="anchor-section" aria-label="Anchor link to header"></a></h2>

diff --git a/docs/regulatory_network_lab.html b/docs/regulatory_network_lab.html
@@ -877,7 +877,7 @@ <h3>Steps<a href="regulatory_network_lab.html#steps" class="anchor-section" aria
 <p>
 you can reuse these iRegulon results by loading this iRF file using
 the ‘Load saved results’ icon <img
-src="Module5/iregulon/images/save2.png" alt="Save2 icon" />..
+src="./Module5/iregulon/images/save2.png" alt="Save2 icon" />..
 </p>
 </div>
 <p>14a)</p>

diff --git a/lectures/Pathways_2024_Module2_ORA_VV.pdf b/lectures/Pathways_2024_Module2_ORA_VV.pdf
diff --git a/lectures/Pathways_2024_finalslides.pdf b/lectures/Pathways_2024_finalslides.pdf
diff --git a/lectures/Pathways_2024_module6_Schwartz.pdf b/lectures/Pathways_2024_module6_Schwartz.pdf
diff --git a/packages.bib b/packages.bib
@@ -28,7 +28,7 @@ @Manual{R-rmarkdown
   title = {rmarkdown: Dynamic Documents for R},
   author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
   year = {2024},
-  note = {R package version 2.27, 
+  note = {R package version 2.26, 
 https://pkgs.rstudio.com/rmarkdown/},
   url = {https://github.com/rstudio/rmarkdown},
 }
-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 @@