Entering edit mode
7.8 years ago
berge2015
▴
110
Hi,
Does anyone know if there is a way to conduct KEGG pathway analysis in edgeR using the Plant database only? Or any other program, for that matter? When I use the kegga function, the results only have human KEGG IDs (hsa*). I however want to use only the information from plant species as I'm working with a plant myself.
I know that a 'manual' method exists: using the KEGG KASS site. But having to export gene list, copy, go through email verification, etc seems not so efficient especially when I want to conduct several analyses.
Thank you for your help.
Which plant are you working on?
Wheat, but I'd like to use multiple plant species for my analysis. Arabidopsis, Rice, Maize, etc.
You can try GeneSCF (easy to use and can run batch jobs).
Do you have the EntrezIDs? Why are you restricted to edgeR?
are you able to comments more if not limited to edgeR by using EntrezID? I was thinking blast my protein dataset to Ath.