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Old 02-08-2012, 06:49 PM   #1
Lisa
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Default pluggin DESeq into Galaxy

I am wondering if anyone have experience to put R scripts ( like DESeq) in to Galaxy?

Thanks

Lisa
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Old 02-10-2012, 09:09 AM   #2
tnabtaf
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Hi Lisa,

The best way to get answers about Galaxy deployments is to post to the Galaxy-dev list (see http://wiki.g2.bx.psu.edu/Mailing%20Lists). That way about 600 people with some knowledge of Galaxy deployments will see it.

People have installed R packages/scripts in Galaxy:
1) On usegalaxy.org, I believe the whole RGENETICS set of tools are R based.
2) In the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/, the digital_dge package uses edgeR from Bioconductor. There may be others.
3) A group at either Wisconsin or Harvard (can't remember) is specifically interested in using DESeq with Galaxy. A post to the list may get a response from them.

Hope this helps.
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Old 02-10-2012, 05:02 PM   #3
Lisa
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That is absolutely helpful.Thanks. Lisa
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