I have multi-omics data (RNASeq, methylation and mutation) belonging to same sample and I want to do gene set enrichment analysis using all the data at once. What are the tool in R/Bioconductor to do gene set enrichment analysis of multiple omics dataset?
Sorry non-R solution:
With GeneSCF you can keep all the list of genes (multiple files) in a single folder and provide that path in 'geneSCF_batch'. It will perform enrichment analysis for individual list and automatically creats output for every list.
Also choose the tool that regularly update the database/functional information. In that case GenrSCF will give you option of updating the database to current version using 'prepare_database' module before running enrichment analysis.