mitch

The "mitch" R package addresses the need for multi-contrast gene set enrichment analysis, particularly in the context of large and diverse omics datasets. It employs a rank-MANOVA statistical approach to identify gene sets that exhibit joint enrichment across multiple contrasts. The package provides unique visualization features, allowing the exploration of enrichments in up to 20 contrasts. Demonstrated through case studies covering RNA expression profiling, multi-omics integration, benchmarking, and single-cell RNA sequencing, "mitch" showcases its utility. Simulated data comparisons indicate similar accuracy to state-of-the-art tools for single-contrast enrichment analysis and superior accuracy in identifying multi-contrast enrichments.