egeulgen/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>.

Getting started

Package details

AuthorEge Ulgen, Ozan Ozisik
MaintainerEge Ulgen <[email protected]>
LicenseMIT + file LICENSE
Version1.3.1.9000
URL https://github.com/egeulgen/pathfindR
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("egeulgen/pathfindR")
egeulgen/pathfindR documentation built on Nov. 28, 2018, 3:07 p.m.