GSEA and pathway analysis in R

Question

[bookorg]

Hi

I have determined differentially expressed genes from GEO datasets. Now I want to analyze functional enrichment analysis and pathway of that DEG in R. so kindly plz help me in that regards.

[bookorg]

Actually I want to some link of generating GSEA and pathway of my DEG in R

Answer 1

[jared.andrews07]

Tons of options - fgsea, clusterProfiler, enrichR, g:profiler, etc.

Those should get you started.

[bookorg]

if I want to generate pathways from wiki,reactome,kegg,biocarta in R ,so what should i do

[jared.andrews07]

Literally pretty much any of those work. I'd read their vignettes/pages to see which one is the best fit for your use case. pathview is another package that may provide helpful utility and interfaces with the output from some of these packages.

[ATpoint]

Reading the manuals of linked tools is a great start. You will most likely not get spoon-feeding here, just saying.