Closed AlexanderPico closed 5 years ago
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
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.
Script for hands-on portion is done: https://github.com/wikipathways/rWikiPathways/blob/master/vignettes/Pathway-Analysis.Rmd
Still working on intro slides