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.