Other packages > Find by keyword >

pathfindR  

Enrichment Analysis Utilizing Active Subnetworks
View on CRAN: Click here


Download and install pathfindR package within the R console
Install from CRAN:
install.packages("pathfindR")

Install from Github:
library("remotes")
install_github("cran/pathfindR")

Install by package version:
library("remotes")
install_version("pathfindR", "3.0.2")



Attach the package and use:
library("pathfindR")
Maintained by
Ege Ulgen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-03-09
Latest Update: 2025-07-15
Description:
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. .
How to cite:
Ege Ulgen (2018). pathfindR: Enrichment Analysis Utilizing Active Subnetworks. R package version 3.0.2, https://cran.r-project.org/web/packages/pathfindR. Accessed 29 Oct. 2026.
Previous versions and publish date:
(2026-07-09 06:39), 1.0.0 (2018-03-09 13:18), 1.1.0 (2018-05-15 00:43), 1.2.0 (2018-06-10 15:24), 1.2.1 (2018-08-18 00:10), 1.2.2 (2018-10-05 01:00), 1.2.3 (2018-10-26 16:40), 1.3.0 (2018-11-20 12:10), 1.4.0 (2019-11-08 12:40), 1.4.1 (2019-11-15 12:10), 1.4.2 (2019-12-06 12:30), 1.5.0 (2020-06-07 02:00), 1.5.1 (2020-09-20 20:00), 1.6.0 (2020-11-21 14:50), 1.6.1 (2021-01-04 20:40), 1.6.2 (2021-08-21 15:20), 1.6.3 (2021-11-15 10:20), 1.6.4 (2022-08-25 14:30), 2.0.0 (2023-05-06 06:20), 2.0.1 (2023-05-10 09:40), 2.1.0 (2023-05-12 09:10), 2.2.0 (2023-08-21 02:40), 2.3.0 (2023-10-08 22:30), 2.3.1 (2024-01-19 20:10), 2.4.0 (2024-04-28 13:50), 2.4.1 (2024-05-04 17:30), 2.4.2 (2025-02-17 10:30), 2.5.0 (2025-06-15 02:00), 2.5.1 (2025-07-15 13:20), 2.6.0 (2025-09-21 01:00), 2.7.0 (2025-12-22 17:20), 3.0.0 (2026-06-22 21:00), 3.0.1 (2026-06-29 09:40)
Other packages that cited pathfindR R package
View pathfindR citation profile
Other R packages that pathfindR depends, imports, suggests or enhances
Complete documentation for pathfindR
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
personalized2part  
Two-Part Estimation of Treatment Rules for Semi-Continuous Data
Implements the methodology of Huling, Smith, and Chen (2020) , w ...
Download / Learn more Package Citations See dependency  
GEVcdn  
GEV Conditional Density Estimation Network
Implements a flexible nonlinear modelling framework for nonstationary generalized extreme value anal ...
Download / Learn more Package Citations See dependency  
binovisualfields  
Depth-Dependent Binocular Visual Fields Simulation
Simulation and visualization depth-dependent integrated visual fields. Visual fields are measured mo ...
Download / Learn more Package Citations See dependency  
fastRG  
Sample Generalized Random Dot Product Graphs in Linear Time
Samples generalized random product graphs, a generalization of a broad class of network models. Giv ...
Download / Learn more Package Citations See dependency  

29,218

R Packages

247,686

Dependencies

77,281

Author Associations

29,219

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA