Workshop 2: Scripting Pathway Analysis

[AlexanderPico]

• Workshop 2: Scripting pathway analysis and data overlays (for programmers). Covers WikiPathways web services, rWikiPathways and RCy3. Most example will be in R.

[Chris-Evelo]

You might want to include scripting Pathways from R and thus feature RPathVisio. I think that that is in fact a nice tool that will need extensions (which is the link with workshop 4 again) but already can be very useful

[AlexanderPico]

Using the same dataset that Tina will use in Workshop 1, I will perform GSEA in R (providing WP as a source) and/or find an R package that already uses WP. Then I'll showcase rWikiPathways and our web service. Then we'll move into rCy3, including app commands for WikiPathways, IDmapper and CyTargetLinker. If Tina and I select the same pathways to view from our enrichment analyses, then we should end up with similar final figures as well.

• Enrichment package:
  • TopGo
  • GSEABase
  • clusterProfiler: https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#go-over-representation-test
• rWikiPathways
• RCy3
  • WikiPathways app
  • ID mapper
  • CyTargetLinker app

[AlexanderPico]

Script for hands-on portion is done: https://github.com/wikipathways/rWikiPathways/blob/master/vignettes/Pathway-Analysis.Rmd

Still working on intro slides

[AlexanderPico]

Intro slides are here: https://docs.google.com/presentation/d/1l6RN8LBYnR83mudQqg_99PJDZbW71or1IkgXpREJ9cY/edit#slide=id.p