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Old 01-06-2014, 02:28 PM   #16
bigmw
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Join Date: Aug 2013
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gage package has a function, kegg.gsets, to generate updated pathway gene set data in real time for ~ 2300 KEGG species and KEGG Orthology (with species="ko").
gageData package provides kegg and GO gene sets for 4 common research species: human, mouse, rat and budding yeast.
You may want to go through the main vignette and other documents of gage package (besides the RNA-Seq workflow tutorial):
http://bioconductor.org/packages/rel...t/doc/gage.pdf
http://bioconductor.org/packages/rel...html/gage.html

gageData is available:
http://bioconductor.org/packages/rel.../gageData.html
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