Pathways and Network Analysis of -Omics Data 2018
Welcome
Welcome to Pathways and Network Analysis of -Omics Data 2018.
The course schedule can be found here.
Pre-readings, pre-work, and laptop setup instructions can be found here.
We are using Google Classroom for discussion. Join the Class at https://classroom.google.com, select the “+” symbol in the upper right corner, click on “Join Class” and enter the class code provided to you.
The full course notes are available as a single PDF.
Class photo
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Pathway and Network Analysis
Gary Bader
Module 2 Finding Over-Represented Pathways
Veronique Voisin
Lab practical part 1 (g:Profiler)
Module 3: Network Visualization and Analysis with Cytoscape
Gary Bader
Veronique Voisin
Day 2
Module 4: More Depth on Network and Pathway Analysis
Lincoln Stein and Robin Haw
Module 5: Gene Function Prediction
Sara Mostafavi
Day 3
Module 6: Regulatory Network Analysis
Michael Hoffman
Final Thoughts
Veronique Voisin
Integrated Assignment
Additional tutorials
EnrichmentMap (GSEA and g:Profiler) step by step protocol: https://www.biorxiv.org/content/early/2017/12/12/232835 and https://github.com/BaderLab/Cytoscape_workflows
Interacting with Cytoscape using CyRest and command lines (for advanced users): https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/R/advanced-cancer-networks-and-data-rcy3.Rmd
Thank you for attending the Pathway and Network Analysis of Omics Data workshop! Help us make this workshop better by filling out our survey.