layout	permalink	title	header1	header2	image	keywords	description	intructors	length
workshop_main_3day	/PNA_2023	Pathways	Workshop Pages for Students	Pathways and Network Analysis 2023	/site_images/CBW_pathway_icon.jpg	Gene lists, predict gene function, identify master regulators	Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.	Gary Bader, Veronique Voisin, Robin Haw, Micheal Hoffman,Ruth Isserlin	3 days

Welcome

Welcome to Pathways and Network Analysis 2023.

The course schedule can be found here

Meet your faculty here

Pre-workshop Tutorials

Required pre-workshop readings and setup can be found here

Class photo

Pathway and Network Analysis Class of 2023

Day 1

Welcome

Nia Hughes

Module 1: Introduction to Pathway and Network Analysis

Gary Bader

Module 1 Pre-work Lecture
Module 1 Lecture Recording
Module 1 Lecture Slides

Module 2: Finding over-represented pathways in gene lists

Veronique Voisin & Ruth Isserlin

Module 2 Lecture Recording
Module 2 Lecture Slides

Module 2 Lab Slides
Module 2 Lab: g:Profiler
Module 2 Lab: GSEA

Module 3: Network Visualization and Analysis with Cytoscape

Ruth Isserlin

Module 3 Lecture Recording
Module 3 Lecture Slides, Part 1
Module 3 Lecture Slides, Part 2

Module 3 Lab Slides Module 3 Lab: g:Profiler
Module 3 Lab: GSEA
Module 3 Lab: (Bonus) Automation

Day 2

Module 4: More Depth on Pathway and Network Analysis

Lincoln Stein & Veronique Voisin

Module 4 Lecture Recording
Module 4 Lecture Slides

Module 4 Lab Slides
Module 4 Lab

Module 5: Gene Function Prediction

Veronique Voisin

Module 5 Pre-Work Lecture
Module 5 Lecture Recording
Module 5 Lecture Slides

Module 5 Lab: Cytoscape
Module 5 Lab: Web

Day 3

Module 6: Review of the tools in integrated workflow

Veronique Voisin

Module 6 Lecture Slides

Module 6: Review of the Tools Module 6 Lab: scRNA PMBC
Module 6 Lab: scRNA pathway analysis using g:Profiler
Module 6 Lab: scNetViz

Module 6 Integrated Assignment
Module 6 Integrated Assignment Bonus: Automation

Optional Module 7: Regulatory Network Analysis