pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks

Pathway analysis is often the first choice for studying the mechanisms underlying a phenotype. However, conventional methods for pathway analysis do not take into account complex protein-protein interaction information, resulting in incomplete conclusions. Previously, numerous approaches that utilize protein-protein interaction information to enhance pathway analysis yielded superior results compared to conventional methods. Hereby, we present pathfindR, another approach exploiting protein-protein interaction information and the first R package for active-subnetwork-oriented pathway enrichment analyses for class comparison omics experiments. Using the list of genes obtained from an omics experiment comparing…