multiGSEA: A GSEA-based pathway enrichment analysis for multi-omics data

Abstract

Gaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of different tools and algorithms have been developed so far. Among those, the gene set enrichment analysis (GSEA) proved to control both type I and II errors well. In recent years the call for a combined analysis of multiple omics layer became prominent, giving rise to a few multi-omics enrichment tools. Each of which has its own drawbacks and restrictions regarding its universal application. Here, we present the multiGSEA package aiding to calculate a combined GSEA-based pathway enrichment on multiple omics layer. The package queries 8 different pathway databases and relies on the robust GSEA algorithm for a single-omics enrichment analysis. In a final step, those scores will be combined to create a robust composite multi-omics pathway enrichment measure. multiGSEA supports 11 different organisms and includes a comprehensive mapping of transcripts, proteins, and metabolite IDs. It is publicly available under the GPL-3 license at https://github.com/yigbt/multiGSEA and at Bioconductor: https://bioconductor.org/packages/multiGSEA.