Enrichment of pathways, reactome, known networks in rice

Question

[zhang.jianhai]

Hello,

I want to do functional enrichment of pathways, reactome, or known networks in rice RNA-seq data using R programming. I need tools that can be used in an automatic manner, since I have many predicted networks to analyse. It seems many tools cannot be used in an automatic way and many automatic tools do not directly use rice gene ids like "LOC_OsXXg" or "OsXXg", which are the 2 most common rice gene IDs.

My question is what are the R-based tools for such enrichments in rice, which can be used in an automatic manner? Preferably they input "LOC_OsXXg" or "OsXXg" ids rather than other ids. As long as it is a tool of an R package that's fine.

Thanks!

[Mark]

You won't find a R tool dedicated to non-model organisms that can compute or perform those functions. There are plenty of tools available that work with specific databases such as KEGG, but you need to do the leg work to find the genes of interest. A good starting point is the BiomartR. It should allow you to retrieve data from ensembl.