Enrichment Analysis Utilizing Active Subnetworks
Overview
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.
Minor Changes and Bug Fixes
- Fixed tests after
pathfindR.data@2.2.0release with change in structure of
example_active_snws data
From NEWS.md in the release
Install
Health
ERRORpackage dependenciesr-oldrel-macos-arm64
Package required but not available: ‘ggkegg’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
- ERROR12 OK, 1 ERRORNow
- ERROR11 OK, 3 ERROR2026-03-10
Documentation
- Help pages
- 65includes a package overview page
- Examples that run
- 59%20 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 13 never run
- Exported functions with examples
- 91%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Downloads
Repository
- PRs merged (all time)
- 85%
- Median days to close, 50 most recently updated closed issues
- 1
- Median days to close, 50 most recently updated closed PRs
- 0
Stars over time
Forks over time
Releases over time
Issues over time
PRs over time
Commits over time
13 development-tooling and community-health practices detected across 6 families in the upstream repository
Checks run against github.com/egeulgen/pathfindr on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-09-17 · The repository has a site deploy workflow
pkgdown site last built 2026-09-17
Show all practicesHide 2 practices
Dependencies
Installing pathfindR adds 90 packages (46 with compiled code, 87 MB of source tarballs). Heaviest: stringi 11 MB, pathfindR.data 6.6 MB, ggplot2 6.0 MB. 2 more not on CRAN are not measured.
Code & Tests
Datasets
People & History
Pick two releases to compare their code metrics.
- 3.0.2Latest
- 3.0.12026-06-29 · diff ↗
- RR 4.6.0 released · 2026-04-24
- 3.0.02025-12-22 · diff ↗ ·
removed 4 exports
active_snw_search, fetch_gene_set, filterActiveSnws, term_gene_graphadded 8 exports
active_subnetwork_search, build_network, build_score_context, create_term_gene_graph, create_term_gene_plot, fetch_gene_sets, filter_active_subnetworks, get_active_subnetworks - 2.7.02025-12-22 · diff ↗
- 2.6.02025-09-21 · diff ↗
- 2.5.12025-07-15 · diff ↗
- 2.5.02025-06-15 · diff ↗
- RR 4.5.0 released · 2025-04-11
- 2.4.22025-02-17 · diff ↗
- 2.4.12024-05-04 · diff ↗
- 2.4.0
- RR 4.4.0 released · 2024-04-24
- 2.3.12024-01-19 · diff ↗
- 2.3.02023-10-08 · diff ↗
- 2.2.02023-08-21 · diff ↗
Show 27 earlier eventsHide 27 earlier events
- 2.1.02023-05-12 · diff ↗
- 2.0.12023-05-10 · diff ↗
- 2.0.02023-05-06 · diff ↗
- RR 4.3.0 released · 2023-04-21
- 1.6.42022-08-25 · diff ↗
- RR 4.2.0 released · 2022-04-22
- 1.6.32021-11-15 · diff ↗
- 1.6.22021-08-21 · diff ↗
- RR 4.1.0 released · 2021-05-18
- 1.6.12021-01-04 · diff ↗
- 1.6.02020-11-21 · diff ↗
- 1.5.12020-09-20 · diff ↗
- 1.5.02020-06-07 · diff ↗ ·
removed 1 export
check_java_versionadded 7 exports
UpSet_plot, combine_pathfindR_results, combined_results_graph, get_gene_sets_list, get_pin_file, term_gene_heatmap, visualize_active_subnetworks - RR 4.0.0 released · 2020-04-24
- 1.4.22019-12-06 · diff ↗
- 1.4.1
- 1.4.02019-11-08 · diff ↗ ·
removed 7 exports
annotate_pathway_DEGs, calculate_pw_scores, cluster_pathways, fuzzy_pw_clustering, hierarchical_pw_clustering, visualize_pw_interactions, visualize_pwsadded 9 exports
annotate_term_genes, cluster_enriched_terms, fetch_gene_set, fuzzy_term_clustering, hierarchical_term_clustering, score_terms, term_gene_graph, visualize_term_interactions, visualize_terms - RR 3.6.0 released · 2019-04-26
- 1.3.02018-11-20 · diff ↗ ·
removed 4 exports
calculate_pwd, choose_clusters, parseActiveSnwSearch, pathmapadded 14 exports
active_snw_search, annotate_pathway_DEGs, cluster_graph_vis, cluster_pathways, create_kappa_matrix, enrichment_analyses, filterActiveSnws, fuzzy_pw_clustering, hierarchical_pw_clustering, hyperg_test, summarize_enrichment_results, visualize_hsa_KEGG, visualize_pw_interactions, visualize_pws - 1.2.32018-10-26 · diff ↗
- 1.2.22018-10-05 · diff ↗
- 1.2.12018-08-18 · diff ↗
- 1.2.02018-06-10 · diff ↗ ·
removed 1 export
cluster_pathwaysadded 4 exports
calculate_pw_scores, calculate_pwd, enrichment_chart, plot_scores - 1.1.02018-05-15 · diff ↗
- RR 3.5.0 released · 2018-04-23
- 1.0.02018-03-09
- RR 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
Cite
Cite this package
Run in R for the authors' entry:
citation("pathfindR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.3389/fgene.2019.00858.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.