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", "2.4.2")
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
pathfindR.data . 10.32614/CRAN.package.pathfindR . https://github.com/egeulgen/pathfindR/issues . https://egeulgen.github.io/pathfindR/ . https://github.com/egeulgen/pathfindR . pathfindR citation info . pathfindR results . pathfindR.pdf . Comparing Two pathfindR Results . Introduction to pathfindR . Step-by-Step Execution of the pathfindR Enrichment Workflow . pathfindR Analysis for non-Homo-sapiens organisms . Visualization of pathfindR Enrichment Results . pathfindR_2.4.2.tar.gz . pathfindR_2.4.2.zip . pathfindR_2.4.2.zip . pathfindR_2.4.1.zip . pathfindR_2.4.1.tgz . pathfindR_2.3.1.tgz . pathfindR_2.4.2.tgz . pathfindR_2.3.1.tgz . pathfindR_2.3.1.tgz . pathfindR archive . https://CRAN.R-project.org/package=pathfindR .
First Published: 2018-03-09
Latest Update: 2024-01-19
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 2.4.2, https://cran.r-project.org/web/packages/pathfindR. Accessed 10 Apr. 2025.
Previous versions and publish date:
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)
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
xtermStyle
Can be used for coloring output in terminals.
It was developed for the standard Ubuntu terminal but ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Christofer Backlin (view profile)
r2resize
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Obinna Obianom (view profile)
txtq
This queue is a data structure that lets parallel processes send and receive messages, and it can he ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: William Michael Landau (view profile)
ecochange
Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biolo ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Wilson Lara Henao (view profile)
GRNNs
This General Regression Neural Networks Package uses various distance functions.
It was motivated b ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Shufeng LI (view profile)
webglobe
Displays geospatial data on an interactive 3D globe in the web browser. ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Richard Barnes (view profile)
24,012
R Packages
207,311
Dependencies
64,867
Author Associations
24,013
Publication Badges
