R code for GO terms and KEGG

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2.7 years ago

iibrams07 ▴ 10

I would like to use R code in order to do a gene set enrichment analysis by going through GO terms (e.g. in DAVID) and KEGG pathways. Is there code in R publicly available that one can use?

Thanks

KEGG GO R • 1.4k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 2.7 years ago by iibrams07 ▴ 10

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clusterprofiler manual here: https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-go.html for GO and for KEGG, https://yulab-smu.top/biomedical-knowledge-mining-book/clusterprofiler-kegg.html

ADD REPLY • link 2.7 years ago by cpad0112 21k

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Thanks. I can unfortunately not run the code since I get the error message Error in library("KEGG") : there is no package called ‘KEGG’. I tried to install KEGG via Bioconductor. I get the error message ' package ‘KEGG’ is not available for Bioconductor version '3.14'. Can you give me an advice how to overcome this ? `

ADD REPLY • link 2.7 years ago by iibrams07 ▴ 10

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There are quite a few tools available to do what you want, each with their own pros and cons. I use g:profiler2 and topGO. You can use any organism with the former, but the latter of which requires an orgDB package.

Regarding code, there are plenty of tutorials a simple google search away, or you can probably find quite a few on GitHub without too much difficulty.

ADD REPLY • link 2.7 years ago by dthorbur ★ 2.6k

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