Where can I get bovine 'kegg.gs' in R?

Question

[mbk0asis]

Hi, all!

I'm trying to do the pathway analysis from bovine RNA-seq data using 'gage' in R, but I couldn't find the 'kegg gene set' for bovine.

If anyone knows how to obtain it, please help me!

Thank you!

Answer 1

[bigmawen]

In gage package, you can use kegg.gsets function to generate kegg pathway gene set data or ~3000 KEGG species, and go.gsets function to generate GO gene set data for 19 major species. Unlike the ones provides with gage and gageData, these gene set data are most up-to-date ones. For details, check:

?kegg.gsets

?go.gsets

The main vignette of gage also showed some example in these functions: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

Answer 2

[EagleEye]

Try GeneSCF,

http://genescf.kandurilab.org/index.php