pathfindR: Pathway Enrichment Analysis Utilizing Active Subnetworks

Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways and to score the pathways per sample. The method is described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. <doi:10.1101/272450>.

Version: 1.3.0
Depends: R (≥ 3.4), knitr, pathview
Imports: AnnotationDbi, DBI, doParallel, foreach, rmarkdown, org.Hs.eg.db, ggplot2, fpc, grDevices, igraph
Published: 2018-11-20
Author: Ege Ulgen, Ozan Ozisik
Maintainer: Ege Ulgen <egeulgen at gmail.com>
BugReports: https://github.com/egeulgen/pathfindR/issues
License: MIT + file LICENSE
URL: https://github.com/egeulgen/pathfindR
NeedsCompilation: no
SystemRequirements: Java JVM 1.8
Citation: pathfindR citation info
Materials: NEWS
CRAN checks: pathfindR results

Downloads:

Reference manual: pathfindR.pdf
Vignettes: pathfindR - Step-by-Step (Manual) Execution of the pathfindR Workflow
pathfindR - An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Package source: pathfindR_1.3.0.tar.gz
Windows binaries: r-devel: pathfindR_1.2.3.zip, r-release: pathfindR_1.2.3.zip, r-oldrel: pathfindR_1.3.0.zip
OS X binaries: r-release: not available, r-oldrel: not available
Old sources: pathfindR archive

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