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:	2.4.1
Depends:	R (≥ 4.0), pathfindR.data (≥ 2.0)
Imports:	DBI, AnnotationDbi, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, ggraph, ggupset, fpc, ggkegg, grDevices, httr, igraph, R.utils, msigdbr, knitr
Suggests:	testthat (≥ 2.3.2), covr, mockery
Published:	2024-05-04
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:

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

Downloads:

Package source:	pathfindR_2.4.1.tar.gz
Windows binaries:	r-devel: pathfindR_2.4.1.zip, r-release: pathfindR_2.4.1.zip, r-oldrel: pathfindR_2.4.1.zip
macOS binaries:	r-release (arm64): pathfindR_2.3.1.tgz, r-oldrel (arm64): pathfindR_2.3.1.tgz, r-release (x86_64): pathfindR_2.3.1.tgz, r-oldrel (x86_64): pathfindR_2.3.1.tgz
Old sources:	pathfindR archive

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