Pathways and Network Analysis 2024

Welcome

Welcome to Pathways and Network Analysis 2024.

The course schedule can be found here

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Pre-workshop Tutorials

Required pre-workshop readings and setup can be found here.

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Class photo

Pathway and Network Analysis Class of 2024

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Course Material

Module 1

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

Module 2

Module 2 Lecture Slides
Module 2 Lecture Recording

Module 2 Lab Slides
Module 2 Lab part 1: g:Profiler
Module 2 Lab part 2: GSEA

Module 3

Module 3 part 1 Lecture Slides: Cytoscape
Module 3 part 1 Lecture Recording: Cytoscape
Module 3 part 1 Lab Slides: Cytoscape
Module 3 part 1 Lab: Cytoscape

Module 3 part 2 Lecture Slide: EnrichmentMap
Module 3 part 2 Lecture Recording: EnrichmentMap
Module 3 part 2 Lab Slides: EnrichmentMap
Module 3 part 2.1 Lab: g:Profiler
Module 3 part 2.2 Lab: GSEA

Module 3 Bonus Lab: Automation

Module 4

Module 4 Lecture Recording
Module 4 Lecture Slides

Module 4 Lab Slides
Module 4 Lab: ReactomeFI

Module 5

Module 5 Pre-work Lecture
Module 5 Lecture Recording
Module 5 Lecture Slides

Module 5 Lab: Cytoscape
Module 5 Lab: Web version

Module 6

Module 6 Lecture Recording
Module 6 Lecture Slides

Module 6 Lab: scRNA PBMC
Module 6 Lab: scRNA Glioblastoma
Module 6 Lab: cellPhoneDB
Module 6 Lab: NEST

Module 7

Final Slides
Module 7: Review of the Tools
Module 7: Integrated Assignment
Module 7: Integrated Assignment Bonus - Automation

Optional Module 8: Regulatory Network Analysis
Optional Module 8: Gene Regulation and Motif Analysis Practical Lab/chIP-seq
Optional Module 8: Gene Regulation and Motif Analysis Practical Lab/iRegulon
Optional Module 8: Automated Enrichment and Visualisation Lab using clusterProfiler