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+
+
+
+
+
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+ Module 2: Finding Over-represented Pathways (Veronique Voisin)
+Veronique Voisin and Ruth Isserlin
+ + + + + +-
diff --git a/docs/integrated_assignment.html b/docs/integrated_assignment.html
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+++ b/docs/integrated_assignment.html
@@ -784,7 +784,7 @@
PART 6: iRegulon +
- Add TCF12 and AVEN to the network. diff --git a/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf b/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf index cde9524..0495516 100644 Binary files a/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf and b/docs/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf differ diff --git a/lectures/Pathways_2024_Module3_lab_introduction_RI.pdf b/docs/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf similarity index 70% rename from lectures/Pathways_2024_Module3_lab_introduction_RI.pdf rename to docs/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf index 759028a..942de84 100644 Binary files a/lectures/Pathways_2024_Module3_lab_introduction_RI.pdf and b/docs/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf differ diff --git a/docs/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf b/docs/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf new file mode 100644 index 0000000..75b67d2 Binary files /dev/null and b/docs/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf differ diff --git a/docs/module-2-finding-over-represented-pathways-veronique-voisin.html b/docs/module-2-finding-over-represented-pathways-veronique-voisin.html new file mode 100644 index 0000000..6c3d5e4 --- /dev/null +++ b/docs/module-2-finding-over-represented-pathways-veronique-voisin.html @@ -0,0 +1,695 @@ + + + + + + +
Module 2: Finding Over-represented Pathways (Veronique Voisin) | Pathway and Network Analysis of -Omics Data ( June 2024 ) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/module-3-network-visualization-and-analysis-with-cytoscape.html b/docs/module-3-network-visualization-and-analysis-with-cytoscape.html index 8c80415..730da08 100644 --- 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 @@Module 3: Network Visualization and Analysis with Cytoscape
Ruth Isserlin
- - -Module 3 Lab
-Ruth Isserlin
- +Module 3 Cytoscape
+ +Module 3 Cytoscape Lab
+Introduction to practical Cytoscape Lab (slides)
Lab practical Cytoscape Primer
+
+Module 3 Enrichment Map
+ +Module 3 Enrichment Map Lab
+Introduction to practical EM Lab (slides)
Lab practical part 1 (g:Profiler)
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt new file mode 100644 index 0000000..bd2704a --- /dev/null +++ b/docs/reference-keys.txt @@ -0,0 +1,334 @@ +canadian-bioinformatics-workshops +welcome +meet-your-faculty +gary-bader +lincoln-stein +gregory-schwartz +veronique-voisin +ruth-isserlin +chaitra-sarathy-phd +nia-hughes +class-materials +schedule +pre-workshop +laptop-setup-instructions +basic-programs +cytoscape-installation +gsea-installation +docker-installation +pre-workshop-tutorials +cytoscape-preparation-tutorials +r-tutorial +pre-workshop-readings-and-lectures +additional-tutorials +intro +module-2-finding-over-represented-pathways-veronique-voisin +gprofiler-lab +introduction +goal-of-the-exercise-1 +data +exercise-1 +step-1---launch-gprofiler. +step-2---input-query +step-3---adjust-parameters. +step-4---run-query +step-5---explore-the-results. +step-6-expand-the-stats-tab +step-7-save-the-results +step-8-optional-but-recommended +option-1-manually-if-you-are-not-familiar-with-unix-commands +option-2-using-the-cat-command-if-you-are-familiar-with-unix-commands +step-9-optional-by-recommended +exercise-2-load-and-use-a-custom-.gmt-file-and-run-the-query +optional-steps +optional-1 +option-2 +option-3 +bonus---automation. +gsea-lab +introduction-1 +goal-of-the-exercise +data-1 +how-was-the-data-processed +background +rank-file +how-to-generate-a-rank-file. +calculation-of-the-score +generation-of-the-rank-file +pathway-defintion-file +start-the-exercise +step1. +step-2. +step3. +step-4. +step-5. +basal +classical +additional_information +bonus---automation.-1 +module-3-network-visualization-and-analysis-with-cytoscape +cytoscape_mod3 +goal-of-the-exercise-2 +data-2 +start-the-exercise-1 +exercise-1a---create-network-from-table +exercise-1b---load-node-attributes +exercise-1c---map-node-attributes-to-visual-style +exercise-2---work-with-larger-networks +exercise-3---perform-basic-enrichment-analysis-using-enrichmenttable +enrichmenttabl-features +exercise-4---load-network-from-ndex +gprofiler_mod3 +goal-of-the-exercise-3 +data-3 +enrichmentmap +description-of-this-exercise +start-the-exercise-2 +exercise-1a---compare-different-gprofiler-geneset-size-results +step-1 +step-2 +step3-explore-the-results +explore-detailed-results +exercise-1b---is-specifying-the-gmt-file-important +exercise-1c---create-em-from-results-using-baderlab-genesets +exercise-1d-optional---investigate-individual-pathways-in-genemania-or-string +genemania +string +bonus---automation.-2 +gsea_mod3 +goal-of-the-exercise-4 +data-4 +enrichmentmap-1 +exercise-1---gsea-output-and-enrichmentmap +step-1-1 +step-2-1 +step-3 +step-4 +exercise-2---post-analysis-add-drug-target-gene-sets-to-the-network +step-5 +exercise-3---autoannotate-the-network +step-6 +exercise-4-optional---explore-results-in-genemania-or-string +step-7 +bonus---automation.-3 +automation +goal-of-the-exercise-5 +set-up---option-1---install-rrstudio +set-up---option-2---docker-image-with-rrstudio +what-is-docker +docker---basic-term-definition +container +image +docker-volumes +r_docker +windows +macos-linux +create-your-first-notebook-using-docker +start-coding +start-using-automation +running-example-notebooks-in-local-rstudio +step-1---launch-rstudio +step-2---create-a-new-project +step-3---open-example-rnotebook +step-4---step-through-notebook-to-run-the-analysis +exercises +additional-resources +module-4-in-depth-analysis-of-networks-and-pathways +ReactomeFI +goal-of-this-practical-lab +data-download-the-following-files-on-your-computer-before-starting-the-practical-lab. +exercise-1-use-the-reactome-functional-interaction-fi-network +question-1-describe-the-size-and-composition-of-the-network +question-2-after-clustering-how-many-modules-are-there +query-information-about-the-interaction-between-2-genes +question-3-what-are-the-most-significant-pathways-in-each-module +set-the-size-of-the-nodes-proportional-to-the-mutation-frequencies-in-each-cancer +play-around-with-the-styles-change-transparency-and-colors +create-a-pie-chart +create-a-subnetwork +fetch-cancer-drugs-on-the-created-subnetwork +save-the-network-as-an-image-for-publication +exercise-2a-explore-reactome-pathways +exercise-2b-pathway-enrichment-analysis-using-a-simple-gene-list +question-1-what-are-the-most-significant-biological-pathways-based-on-the-fdr +answer-to-question-1 +exercise-2c-pathway-based-analysis-using-a-rank-gene-list-gsea +automation-for-advanced-users +reference-guide-bonus-exercises +module-5-gene-function-prediction +genemania_cytoscape +goal-of-this-practical-lab-1 +exercise-1-searching-genemania-with-single-gene +answers +exercise-2-searching-genemania-with-gene-list +exercise-3-searching-genemania-with-mixed-gene-list +genemania-definitions +in-advanced-options +exercise-4-optional-discover-the-stringapp +more-string-information-and-tutorials +genemania_web +goal-of-this-practical-lab-2 +exercise-1-questions-and-steps-to-follow +exercise-1-answers-detailed-explanation-and-screenshots +exercise-1---steps-1-4 +exercise-1---step-5 +exercise-1---step-6 +exercise-1---step-7 +exercise-1---step-8 +exercise-1---step-9 +exercise-1---step-10-layouts +circular-layout +aligned-layout +force-directed-layout +exercise-1---step-11-save-an-image +exercise-2-questions-and-steps-to-follow +exercise-2-answers-detailed-steps-and-screenshots +exercise-2---steps-1-to-4 +exercise-2---step-5 +exercise-2---step-6. +exercise-2---step-7 +exercise-2---step-8 +exercise-2---step-9 +exercise-2---step-10 +exercise-2---step-11 +exercise-2---step-12 +exercise-2---step-13. +exercise-3-questions-and-steps-to-follow +exercise-3-more-details-and-screenshots +exercise-3---steps-1---3 +exercise-3---step-4-step5 +exercise-3---steps-6 +exercise-3---step-7 +exercise-3---step-8 +exercise-3---step-9 +some-definitions +in-advanced-options-1 +module-6-cell-cell-communication +module-6-lecture-cell-cell-communication. +scrna-lab-praticals +scRNA_PBMC +introduction-2 +pmbc3k-seurat-pipeline +load-libraries +load-the-pbmc-dataset +process-the-dataset +assign-cell-type-identity-to-clusters +find-differentially-expressed-features-cluster-biomarkers +create-gene-list-for-each-cluster-to-use-with-gprofiler +tutorial_start +run-pathway-enrichment-analysis-using-gprofiler +create-an-enrichment-map-in-cytoscape +gsea-from-pseudobulk +pseudobulk-creation-differential-expression-and-rank-file +run-gsea +create-an-enrichmentmap +scRNA_glioblastoma +introduction-3 +goal +data-5 +overview +can-module8-exercise-1 +step-1---launch-gprofiler.-1 +step-2---input-query-1 +step-3---adjust-parameters.-1 +step-4---run-query-1 +step-5---explore-the-results.-1 +step-6-expand-the-stats-tab-1 +step-7-save-the-results-1 +step-8-optional-but-recommended-1 +exercise-2 +goal-of-the-exercise-6 +data-6 +enrichmentmap-2 +description-of-this-exercise-1 +start-the-exercise-3 +step-1-2 +step-2-2 +step-3-explore-detailed-results +step-4-optional-autoannotate-the-enrichment-map +exercise-3 +goal-1 +data-7 +start-the-exercise-4 +step-1-3 +step-2-3 +scRNA_cellPhoneDB +cell-cell-communication-in-scrna-cellphonedb +presentation +method +examining-the-results +visualization-using-cytoscape +dataset-and-references +dataset_prep +scRNA_NEST +cell-cell-communication-ccc-in-spatial-transcriptomics-using-nest +presentation-of-nest-neural-network-on-spatial-transcriptomics +how-to-run-nest +practical-lab-pancreatic-ductal-adenocarcinoma-pdac +module-7-review-of-the-tools +final-slides +scrna-lab-praticals-1 +integrated-assignment +integrated-assignment-bonus +integrated_assignment +goal-2 +dataset-1 +background-1 +data-processing +part-1-run-gprofiler +part-2-save-as-generic-enrichment-map-output-be +part-3-save-as-generic-enrichment-map-output-ne +part-4-create-an-enrichment-map +answers-gprofiler +part-5-gsea-run-and-create-an-enrichment-map +part-6-iregulon +dataset-2 +part-1-reactomefi +answers-reactome-fi +part-2-genemania +answers-genemania +ass_automation +goal-of-the-exercise-7 +intro-regulatory-networks +lecture +practical-lab-1-chip_seq-data---great-and-meme-chip +practical-lab-2-gene-list---iregulon-and-enrichrenrichmentmap +additional-slides-about-the-tools-segway-and-behst-presented-during-the-lecture +regulatory_network_chipseq_lab +goal-of-this-practical-lab-3 +dataset-used-during-this-practical-lab +exercise-1---run-pathway-analysis-using-great +perform-pathway-enrichment +explore-the-results. +perform-pathway-enrichment---proximal-approach +explore-the-results.---proximal-analysis +exercise-2---build-an-enrichment-map-to-visualize-great-results +exercise-3-optional-practice-building-enrichment-maps-and-auto-annotation +optional-exercise-3a-autoannotate-the-enrichment-map +optional-exercise-3b-repeat-the-process-of-building-an-enrichment-map-using-the-proximal-data-proximal_gobp_greatexportall.tsv. +optional-exercise-3c-repeat-the-process-by-building-both-the-proximal-and-distal-enrichment-maps-at-the-same-time. +exercise-4-add-runx1-targets-and-runx1-ko-genes-on-the-distal-enrichment-map. +step-4a-post-analysis +step-4b-optional-change-the-edge-style-of-the-signature-gene-sets +exercise-5-learning-how-to-run-meme-chip-from-the-meme-suite-httpsmeme-suite.orgmemetoolsmeme-chip +format-the-data +exercise-5a-download-sequences-from-.bed-coordinates +exercise-5b-run-meme-chip +exercise-6-optional-get-the-iregulon-runx1-targets-and-find-the-mouse-orthologs-using-gorth-from-gprofiler-to-create-the-gmt-file-used-in-exercise-4. +end-of-lab +regulatory_network_lab +iregulon-lab +goal-3 +exercise-1.-detect-regulons-from-co-expressed-genes +skills-learned-in-this-exercise +steps +exercise-2.-create-a-metatargetome-using-iregulon-and-merge-2-networks-in-cytoscape. +end-of-exercise +use-our-precomputed-iregulon-results +notes-about-iregulon +motif-oriented-view +notes-about-cytoscape +exercise-3.-use-enrichr-with-the-prostate-gene-list. +goal-4 +steps-1 +end-of-practical-lab diff --git a/docs/regulatory_network_lab.html b/docs/regulatory_network_lab.html index a139c36..99bd2df 100644 --- a/docs/regulatory_network_lab.html +++ b/docs/regulatory_network_lab.html @@ -877,7 +877,7 @@Steps you can reuse these iRegulon results by loading this iRF file using the ‘Load saved results’ icon
.. +src="Module5/iregulon/images/save2.png" alt="Save2 icon" />..
14a)
diff --git a/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf b/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf index cde9524..0495516 100644 Binary files a/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf and b/lectures/Pathways_2024_Module2_lab_introduction_RI.pdf differ diff --git a/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf b/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf new file mode 100644 index 0000000..942de84 Binary files /dev/null and b/lectures/Pathways_2024_Module3_EM_lab_introduction_RI.pdf differ diff --git a/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf b/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf new file mode 100644 index 0000000..75b67d2 Binary files /dev/null and b/lectures/Pathways_2024_Module3_cytoscape_lab_introduction_RI.pdf differ diff --git a/packages.bib b/packages.bib index e055833..1613a08 100644 --- 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 2.26, + note = {R package version 2.27, https://pkgs.rstudio.com/rmarkdown/}, url = {https://github.com/rstudio/rmarkdown}, }