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?
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
