Best R package for GO and KEGG enrichment

[Doug]

Hi all,

I am looking for an R package for Gene Ontology enrichment. Basically, I want to give it a background list of genes and a foreground list of genes and test for enrichment in the foreground. Ideally, it would also do KEGG pathway enrichment and allow me to toggle on/off whether to include or remove duplicate genes. There seem to be a several different packages out there. I am looking for the best/easiest to use. Thanks.

[Kambiz]

Hi Doug

Have you not considered to use DAVID software (http://david.abcc.ncifcrf.gov/). It does what you asking for. Additionlly, it will give you statistical value on the enriched group based on Fisher exact ... It gives other informations also beside GO and KEGG ...

Success,
Kambiz