I have a couple hundred nucleotide sequences from a Fungus genome. I want to perform KEGG pathway analysis preferably using R package. Could anyone please suggest me any good R package?
I would suggest KEGGprofile or KEGGrest
You can also do that using edgeR
That's great, I didn't know... very useful if you are already using edgeR!
check ClusterProfiler http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html and document link http://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
enrichR is a pretty good tool
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