BioLion has asked for the wisdom of the Perl Monks concerning the following question:
Dear Monks,
A bioinformatics question: I have been doing more and more Gene Ontology (GO) work, specifically, I am looking for enriched terms in my various gene sets. I usually go through the web-based programs like DAVID or Babelomics.
However, I now need a high-throughput approach, but was disappointed to only find GO::TermFinder on CPAN.
There are plenty of GO handlers/parsers available, but far fewer analytical tools, so I wondered if anyone had any experience of doing GO term enrichment on many many groups of genes?
- Any particular API I should use?
- Any particular problems I should look out for?
- Is there another web-based program I should think about?
- Is there a downloadable program that might be a good alternate? (i.e. a commandline based one that I can use via perl)
NB: I have cross-posted a similar question on seqAnswers in an attempt to keep this one BioPerl/perl related...
Just a something something...
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Replies are listed 'Best First'. | |
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Re: BioPerl: Best Gene Ontology API
by tospo (Hermit) on Aug 23, 2010 at 11:58 UTC | |
by BioLion (Curate) on Aug 23, 2010 at 13:09 UTC | |
Re: BioPerl: Best Gene Ontology API
by zentara (Archbishop) on Aug 23, 2010 at 11:57 UTC | |
by BioLion (Curate) on Aug 23, 2010 at 13:17 UTC | |
Re: BioPerl: Best Gene Ontology API
by lima1 (Curate) on Aug 23, 2010 at 17:33 UTC | |
by BioLion (Curate) on Aug 23, 2010 at 17:38 UTC | |
by lima1 (Curate) on Aug 23, 2010 at 17:49 UTC | |
by BioLion (Curate) on Aug 24, 2010 at 08:39 UTC | |
Re: BioPerl: Best Gene Ontology API
by Anonymous Monk on Aug 25, 2010 at 17:39 UTC |
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