pathfindR

3.0.2

Enrichment Analysis Utilizing Active Subnetworks

0packages depend

14.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Ege UlgenFirst published 2018-03-0933 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("pathfindR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("egeulgen/pathfindR")

Development version from egeulgen/pathfindR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pathfindr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

1ERROR1NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-arm64

Slowest check: 12.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.79

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-03-10
11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 59%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

14.3K

CRAN downloads in the past year

Rank #3,346 · ~39/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.5K90 days

14.3K1 year

Compare downloads with other packages →

Also on169 r2u1.8K bioconda22 c2d4u

Repository

GitHub ↗ egeulgen/pathfindr

202Stars

27Forks

0Open issues

0Open PRs

35Releases

1,114Commits

5Contributors

pathwaysubnetworkenrichmentpathway-enrichment-analysisactive-subnetworksr

1,114 commits · Last activity 2026-07-02 · 0% stars, 30d

Stars over time

2025-06-19 · 1902026-07-16 · 201

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/egeulgen/pathfindr on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Coverage (1)

Codecov

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.3.0pathfindR.data

Imports (18)

DBI AnnotationDbi doParallel foreach rmarkdown ggplot2 ggraph ggupset ggnewscale fpc ggkegggrDeviceshttr igraph R.utils msigdbr knitr Rcpp

LinkingTo (1)

Rcpp

Suggests (4)

org.Hs.eg.db testthat covr mockery

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Ege Ulgen

Maintainer, Copyright holder

Authors (1)

Ozan Ozisik

Author

Ege Ulgen

Maintainer, Copyright holder

Package Timeline

33 releases. Pick two to compare their code metrics. R releases are shown for context.

3.0.2Latest
2026-07-02 · current release · diff ↗
3.0.1
2026-06-29 · diff ↗
3.0.0
2026-06-22 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.7.0
2025-12-22 · diff ↗
2.6.0
2025-09-21 · diff ↗
2.5.1
2025-07-15 · diff ↗
2.5.0
2025-06-15 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.4.2
2025-02-17 · diff ↗
2.4.1
2024-05-04 · diff ↗
2.4.0
2024-04-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.3.1
2024-01-19 · diff ↗
2.3.0
2023-10-08 · diff ↗
2.2.0
2023-08-21 · diff ↗

Show 27 earlier events

2.1.0
2023-05-12 · diff ↗
2.0.1
2023-05-10 · diff ↗
2.0.0
2023-05-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6.4
2022-08-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.6.3
2021-11-15 · diff ↗
1.6.2
2021-08-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.6.1
2021-01-04 · diff ↗
1.6.0
2020-11-21 · diff ↗
1.5.1
2020-09-20 · diff ↗
1.5.0
2020-06-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.4.2
2019-12-06 · diff ↗
1.4.1
2019-11-15 · diff ↗
1.4.0
2019-11-08 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.0
2018-11-20 · diff ↗
1.2.3
2018-10-26 · diff ↗
1.2.2
2018-10-05 · diff ↗
1.2.1
2018-08-18 · diff ↗
1.2.0
2018-06-10 · diff ↗
1.1.0
2018-05-15 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.0
2018-03-09
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-09
Total releases: 33 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3.0
Bundled data: 28 KB / 1 file
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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