Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Version: 2.5.0 Depends: R (≥ 4.3.0), pathfindR.data (≥ 2.0) Imports: DBI, AnnotationDbi, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, ggraph, ggupset, fpc, ggkegg (≥ 1.4.0), grDevices, httr, igraph, R.utils, msigdbr (≥ 24.1.0), knitr Suggests: testthat (≥ 2.3.2), covr, mockery Published: 2025-06-15 DOI: 10.32614/CRAN.package.pathfindR Author: Ege Ulgen [cre, cph], Ozan Ozisik [aut] Maintainer: Ege Ulgen <egeulgen at gmail.com> BugReports: https://github.com/egeulgen/pathfindR/issues License: MIT + file LICENSE URL: https://egeulgen.github.io/pathfindR/, https://github.com/egeulgen/pathfindR NeedsCompilation: no SystemRequirements: Java (>= 8.0) Citation: pathfindR citation info Materials: NEWS In views: Omics CRAN checks: pathfindR results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=pathfindR to link to this page.
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