CRAN/E | pathfindR

pathfindR

Enrichment Analysis Utilizing Active Subnetworks

Installation

About

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.

Citation pathfindR citation info
egeulgen.github.io/pathfindR/
github.com/egeulgen/pathfindR
System requirements Java (>= 8.0)
Bug report File report

Key Metrics

Version 2.4.1
R ≥ 4.0
Published 2024-05-04 156 days ago
Needs compilation? no
License MIT
License File
CRAN checks pathfindR results

Downloads

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Maintainer

Maintainer

Ege Ulgen

Authors

Ege Ulgen

cre / cph

Ozan Ozisik

aut

Material

NEWS
Reference manual
Package source

In Views

Omics

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

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

pathfindR archive

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