I have used Go::TermFinder in the past and it worked fine for me for enrichment analyses, basically as desribed in the documentation for the module.

Might also be worth to post to the BioPerl mailing list: http://www.bioperl.org/wiki/Mailing_lists

In reply to Re: BioPerl: Best Gene Ontology API by tospo
in thread BioPerl: Best Gene Ontology API by BioLion

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