pathfindR: Enrichment Analysis Utilizing Active Subnetworks

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: 1.5.0
Depends: R (≥ 4.0),
Imports: DBI, AnnotationDbi, doParallel, foreach, rmarkdown,, ggplot2, ggraph, ggupset, fpc, grDevices, igraph, R.utils, magick, msigdbr, KEGGREST, KEGGgraph, knitr
Suggests: testthat (≥ 2.3.2), covr
Published: 2020-06-07
Author: Ege Ulgen ORCID iD [cre, cph], Ozan Ozisik ORCID iD [aut]
Maintainer: Ege Ulgen <egeulgen at>
License: MIT + file LICENSE
NeedsCompilation: no
SystemRequirements: Java (>= 8.0)
Citation: pathfindR citation info
Materials: NEWS
CRAN checks: pathfindR results


Reference manual: pathfindR.pdf
Vignettes: Comparing Two pathfindR Results
Introduction to pathfindR
Step-by-Step Execution of the pathfindR Enrichment Workflow
pathfindR Analysis for non-Homo-sapiens organisms
Obtaining PIN and Gene Sets Data
Visualization of pathfindR Enrichment Results
Package source: pathfindR_1.5.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: not available, r-oldrel: not available
Old sources: pathfindR archive


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