I have ChIP-Seq data stemming from 3 samples, each with 3 replicates and 1 input sample. I ran the ENCODE ChIP-Seq pipeline. After annotation of the reproducible peaks that is generated by IDR, I am trying to do some gene set enrichment analysis on these genes. I have tried to use the following strategies for the same:
1) GSEA: According to the FAQ section of GSEA, ChIP-seq data can be analyzed using the preranked GSEA module however I do not have a huge number gene list that are ranked. I just have a bunch of genes that are ranked by the q value that IDR generates. So there was no particular result that I found here.
2) Chipenrich: I used the hybridenrich function of this software as I have few peaks but there were significant terms that are enriched.
3) clusterProfiler: neither enrichKEGG or enrichGO gave me anything significant either.
Is there a better approach to what I am trying to accomplish?
Thank you, Asma