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GO and KEGG from DESeq2 counts

Does anyone know of a Bioconductor or other R package that can do GO and/or KEGG Gene set enrichment analysis from counts generated with DESeq2? I have a set of counts generated via DESeq2, with some very nice differential expression analysis. I was thinking of redoing the DE analysis using EdgeR which also uses a negative bionomial based normalization, as I could then use the GOana package for GO and KEGG analysis. Can that work with DESeq2, or is there a similar package that can use counts generated in DESeq2?

r rna-seq rna-seq kegg go
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updated by eyonesi • eyonesi • written by devarts • devarts

Just curious to know why edgeR works with GOana whille DESeq2 doesn't. Both gives a list of genes and I have performed GO analysis based on this list on web via DAVID and Panther. What's the difference with R packages?

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written by Arindam Ghosh Arindam Ghosh

1 answer

GOseq is a suitable R package for GO AND KEGG enrichment. Maybe this link will help you related to DESeq2.

https://wikis.utexas.edu/display/bioiteam/GO+Enrichment+using+goseq

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written by eyonesi • eyonesi

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