CBW Pathways Workshop
Canadian Bioinformatics Workshops
Welcome
Module 1 - Introduction to Pathway and Network Analysis (Gary Bader)
Module 2: Finding Over-represented Pathways (Veronique Voisin)
Module 2 lab - g:Profiler
Module 2 lab - GSEA
Module 3: Network Visualization and Analysis with Cytoscape
Module 3 Lab Primer: Cytoscape Primer
Module 3 Lab: g:profiler Visualization
Module 3 Lab: GSEA Visualization
Module 3 Lab: (Bonus) Automation
Module 4: In-depth Analysis of Networks and Pathways
Module 4 Lab: ReactomeFI
Module 5: Gene Function Prediction
Module 5 Lab: GeneMANIA (Cytoscape version)
Module 5 Lab: GeneMANIA (web version)
Module 6: Cell Cell Communication
- Module 6 lecture : Cell-Cell Communication.
- scRNA lab praticals
Module 6 lab 1: scRNA PBMC
Module 6 lab 2- scRNA Glioblastoma
Module 6 lab 3: cellPhoneDB
- Cell-Cell communication in scRNA: CellPhoneDB
Module 6 lab 4: NEST
- Cell-Cell Communication (CCC) in spatial transcriptomics using NEST
Module 7: Review of the tools
Module 7 Integrated Assignment
Module 7 Integrated Assignment Bonus - Automation
- Goal of the exercise:
Optional Module 8: Regulatory Network Analysis
Optional Module 8 Lab 1: Gene Regulation and Motif Analysis Practical Lab /chIP-seq
Optional Module 8 Lab 2: Gene Regulation and Motif Analysis Practical Lab / iRegulon
Optional Module 8 Lab 3: Automated Enrichment and Visualisation Lab using clusterProfiler
Published with bookdown

Pathway and Network Analysis of -Omics Data ( June 2024 )

Module 5: Gene Function Prediction

Veronique Voisin

Recorded video 1

Lab practical - Cytoscape

Lab practical - Web