R package citation, R package reverse dependencies, R package scholars, install an r package from GitHub hy is package acceptance pending why is package undeliverable amazon why is package on hold dhl tour packages why in r package r and r package full form why is r free why r is bad which r package to install which r package has which r package which r package version which r package readxl which r package ggplot which r package fread which r package license where is package.json where is package-lock.json where is package.swift where is package explorer in eclipse where is package where is package manager unity where is package installer android where is package manager console in visual studio who r package which r package to install which r package version who is package who is package deal who is package design r and r package full form r and r package meaning what r package has what package r what is package in java what is package what is package-lock.json what is package in python what is package.json what is package installer do r package can't install r packages r can't find package r can't load package can't load xlsx package r can't install psych package r can't install sf package r Write if else in NONMEM pk pd
pathfindR
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]
[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
Functions, R codes and Examples using
the pathfindR R package
Some associated functions: UpSet_plot . active_snw_enrichment_wrapper . active_snw_search . annotate_term_genes . check_java_version . cluster_enriched_terms . cluster_graph_vis . color_kegg_pathway . combine_pathfindR_results . combined_results_graph . configure_output_dir . create_HTML_report . create_kappa_matrix . download_KGML_file . download_kegg_png . enrichment . enrichment_analyses . enrichment_chart . fetch_gene_set . fetch_java_version . filterActiveSnws . fuzzy_term_clustering . get_biogrid_pin . get_gene_sets_list . get_kegg_gsets . get_mgsigdb_gsets . get_pin_file . get_reactome_gsets . gset_list_from_gmt . hierarchical_term_clustering . hyperg_test . input_processing . input_testing . isColor . obtain_colored_url . pathfindR . plot_scores . process_pin . return_pin_path . run_pathfindR . score_terms . single_iter_wrapper . summarize_enrichment_results . term_gene_graph . term_gene_heatmap . visualize_active_subnetworks . visualize_hsa_KEGG . visualize_term_interactions . visualize_terms .
Some associated R codes: active_snw_search.R . clustering.R . comparison.R . core.R . data_generation.R . enrichment.R . pathfindr.R . scoring.R . utility.R . visualization.R . zzz.R . Full pathfindR package functions and examples
Downloads during the last 30 days
Today's Hot Picks in Authors and Packages
nextGenShinyApps
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Obinna Obianom (view profile)
personalized2part
Implements the methodology of Huling, Smith, and
Chen (2020) , w ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Jared Huling (view profile)
GEVcdn
Implements a flexible nonlinear modelling framework for nonstationary generalized extreme value anal ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Alex J. Cannon (view profile)
binovisualfields
Simulation and visualization depth-dependent integrated visual fields. Visual fields are measured mo ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Ping Liu (view profile)
fastRG
Samples generalized random product graphs, a generalization of
a broad class of network models. Giv ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Alex Hayes (view profile)
29,218
R Packages
247,686
Dependencies
77,281
Author Associations
29,219
Publication Badges
