I have been using goseq for GO term and KEGG pathway enrichment analysis for RNAseq data. My question is if it is possible to use goseq for the same enrichment analyses for Biocarta, Reactome, and NCI pathways?
The graphite package is able to provide these pathways for topological pathway analyses, but I would like to use these pathways for the goseq enrichment approach (where gene length is taking into account).
Is there a simple way to combine or integrate these analyses (goseq with graphite)? Has anyone any experience with this combination?
Thanks in advance!
Benjamin Nota, PhD
Department of Blood Cell Research