ActivePathways: Integrative Pathway Enrichment Analysis of Multivariate Omics Data

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. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. 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 recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.

Version:	2.0.6
Depends:	R (≥ 3.6)
Imports:	data.table, ggplot2
Suggests:	testthat, knitr, rmarkdown, RColorBrewer
Published:	2025-07-11
DOI:	10.32614/CRAN.package.ActivePathways
Author:	Juri Reimand [aut, cre], Jonathan Barenboim [ctb], Mykhaylo Slobodyanyuk [aut]
Maintainer:	Juri Reimand <juri.reimand at utoronto.ca>
BugReports:	https://github.com/reimandlab/ActivePathways/issues
License:	GPL-3
NeedsCompilation:	no
Materials:	NEWS
In views:	Omics
CRAN checks:	ActivePathways results

Documentation:

Reference manual:	ActivePathways.html , ActivePathways.pdf
Vignettes:	ActivePathways (source, R code)

Downloads:

Package source:	ActivePathways_2.0.6.tar.gz
Windows binaries:	r-devel: ActivePathways_2.0.6.zip, r-release: ActivePathways_2.0.6.zip, r-oldrel: ActivePathways_2.0.6.zip
macOS binaries:	r-release (arm64): ActivePathways_2.0.6.tgz, r-oldrel (arm64): ActivePathways_2.0.6.tgz, r-release (x86_64): ActivePathways_2.0.6.tgz, r-oldrel (x86_64): ActivePathways_2.0.6.tgz
Old sources:	ActivePathways archive

Reverse dependencies:

Reverse imports:

DEET, scapGNN

Linking:

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