I would like to perform a pathway analysis in R.
In particular, I have the genes signatures (that define pathways) that I want to investigate.
I have just perform the differential expression analysis between the conditions.
I would like to know, using ONLY deg, which signatures are enriched.
clusterProfiler - actively maintained R package with great documentation. Includes built-in support for GO analysis, but can also plugin GMT files from WikiPathways or even of your own creation.
rSEA - one of the newer options in this space. According to their paper, it resolves a lot of statistical issues with prior approaches. It's also flexible enough to use with GO, WikiPathways or your own GMTs. Note: this method, uses p-values from all genes in your DE analysis (not just a pre-selected subset of DEGs).