Question

GSEA and pathway analysis in R

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2.3 years ago

bookorg ▴ 10

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.

GSEA pathway • 1.3k views

ADD COMMENT • link updated 2.3 years ago by jared.andrews07 ★ 16k • written 2.3 years ago by bookorg ▴ 10

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

ADD REPLY • link 2.3 years ago by bookorg ▴ 10

score 1 · Answer 1 · 2022-01-04

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2.3 years ago

jared.andrews07 ★ 16k

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

Those should get you started.

ADD COMMENT • link 2.3 years ago by jared.andrews07 ★ 16k

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

ADD REPLY • link 2.3 years ago by bookorg ▴ 10

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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.

ADD REPLY • link 2.3 years ago by jared.andrews07 ★ 16k

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

ADD REPLY • link 2.3 years ago by ATpoint 81k