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 25 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

edeaR  
Exploratory and Descriptive Event-Based Data Analysis
Exploratory and descriptive analysis of event based data. Provides methods for describing and select ...
Download / Learn more Package Citations See dependency  
airGRiwrm  
'airGR' Integrated Water Resource Management
Semi-distributed Precipitation-Runoff Modelling based on 'airGR' package models integrating human i ...
Download / Learn more Package Citations See dependency  
sitmo  
Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel enviro ...
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  
foster  
Forest Structure Extrapolation with R
Set of tools to streamline the modeling of the relationship betweensatellite imagery time series or ...
Download / Learn more Package Citations See dependency  

27,535

R Packages

236,180

Dependencies

73,223

Author Associations

27,536

Publication Badges

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