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.
Module 1: Introduction to Pathway and Network Analysis
Module 2 Finding Over-Represented Pathways
Module 3: Network Visualization and Analysis with Cytoscape
Module 4: More Depth on Network and Pathway Analysis
Lincoln Stein and Robin Haw
Module 5: Gene Function Prediction
Module 6: Regulatory Network Analysis
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.