Question: Where can I get bovine 'kegg.gs' in R?
1
gravatar for mbk0asis
3.3 years ago by
mbk0asis460
Korea, Republic Of
mbk0asis460 wrote:

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!

bovine rna-seq kegg.gs • 943 views
ADD COMMENTlink modified 3.3 years ago by EagleEye6.4k • written 3.3 years ago by mbk0asis460
0
gravatar for bigmawen
3.3 years ago by
bigmawen310
United States
bigmawen310 wrote:

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

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by bigmawen310
0
gravatar for EagleEye
3.3 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Try GeneSCF,

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

ADD COMMENTlink written 3.3 years ago by EagleEye6.4k
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