Other packages > Find by keyword >

ActivePathways  

Integrative Pathway Enrichment Analysis of Multivariate Omics Data
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("ActivePathways", "2.0.6")



Attach the package and use:
library("ActivePathways")
Maintained by
Juri Reimand
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-05-04
Latest Update: 2025-07-11
Description:
Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The first version of the package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) .
How to cite:
Juri Reimand (2019). ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. R package version 2.0.6, https://cran.r-project.org/web/packages/ActivePathways. Accessed 05 Jun. 2026.
Previous versions and publish date:
1.0.1 (2019-05-04 12:10), 1.0.2 (2020-07-09 19:20), 1.0.3 (2021-12-03 13:50), 1.0.4 (2022-01-14 05:32), 1.1.0 (2022-04-20 08:32), 1.1.1 (2022-07-08 19:00), 2.0.0 (2023-08-12 00:50), 2.0.2 (2023-10-02 16:10), 2.0.3 (2023-10-31 21:00), 2.0.4 (2024-06-21 23:10), 2.0.5 (2024-07-28 16:30)
Other packages that cited ActivePathways R package
View ActivePathways citation profile
Other R packages that ActivePathways depends, imports, suggests or enhances
Complete documentation for ActivePathways
Functions, R codes and Examples using the ActivePathways R package
Some associated functions: ActivePathways . DPM . GMT . brownsMethod . columnSignificance . enrichmentAnalysis . export_as_CSV . hypergeometric . makeBackground . merge_p_values . orderedHypergeometric . prepareCytoscape . 
Some associated R codes: Full ActivePathways package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

msm  
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal d ...
Download / Learn more Package Citations See dependency  
crossurr  
Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers
Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebau ...
Download / Learn more Package Citations See dependency  
envirem  
Generation of ENVIREM Variables
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables. ...
Download / Learn more Package Citations See dependency  
ibb  
R Wrapper for Istanbul Municipality Open Data Portal
Call wrappers for Istanbul Metropolitan Municipality's Open Data Portal (Turkish: Istanbul B ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

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