I was wondering if someone knows of a tool to perform a pathway analysis with co-variates for RNA-seq data.
What I mean in more detail is the following: I have two groups (cond. 1 vs. cond. 2) but I also have co-variates which will have an high impact on the expression (20-30 samples in total, balanced design). Hence I am not sure that a standard DE analysis e.g. with voom/limma with co-variates will lead to significant results. I more expect that the same pathways will be up or down regulated than particular genes. Hence, I am looking for a gene-set based analysis where I can also give co-variates as parameters.
Thanks for your help!