ActivePathways

2.0.6

Integrative Pathway Enrichment Analysis of Multivariate Omics Data

2packages depend

7.7Kdownloads / year

69.1%test coverage

13/13checks pass

Overview

About

Maintained by Juri ReimandFirst published 2019-05-0412 releasesCRAN page ↗GitHub ↗

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.

Latest changes · 2.0.6

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ActivePathways", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("reimandlab/ActivePathways")

Development version from reimandlab/ActivePathways. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-activepathways

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ActivePathways

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ActivePathways

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.21

69.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 75%
Documented parameters: 94%
Return-value docs: 90%
References docs: 0%

Downloads

7.7K

CRAN downloads in the past year

Rank #6,133 · ~21/day · ~638/mo

Releases R versions

Daily download trend is not available in this view yet.

54030 days

1.5K90 days

7.7K1 year

Compare downloads with other packages →

Also on143 r2u90 autocran10 c2d4u

Repository

GitHub ↗ reimandlab/activepathways

121Stars

26Forks

1Open issues

0Open PRs

0Releases

335Commits

10Contributors

335 commits · Last activity 2025-07-11 · +0.8% stars, 30d

Stars over time

2025-07-16 · 1122026-07-21 · 121

Repository practices

Upstream repositoryBeta

Checks run against github.com/reimandlab/activepathways on 2026-07-30.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (2)

data.table ggplot2

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown RColorBrewer

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

DEET scapGNN

Code & Tests

People & History

People (3)

Maintainer (1)

Juri Reimand

Author, Maintainer

Authors (2)

Juri Reimand

Author, Maintainer

Mykhaylo Slobodyanyuk

Author · added in 1.0.4

Contributors (1)

Jonathan Barenboim

Contributor

Listed in earlier versions (1)

Helen Zhu

no longer listed · 1.0.1

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.0.6Latest
2025-07-12 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.5
2024-07-28 · diff ↗
2.0.4
2024-06-21 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.3
2023-10-31 · diff ↗
2.0.2
2023-10-02 · diff ↗
2.0.0
2023-08-12 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.1
2022-07-08 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
2022-04-20 · diff ↗
1.0.4
2022-01-14 · diff ↗
1.0.3
2021-12-03 · diff ↗
unarchivedReturned to CRAN
2021-12-03

Show 8 earlier events

archivedRemoved from CRAN
2021-10-05
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
1.0.2
2020-07-09 · diff ↗
unarchivedReturned to CRAN
2020-07-09
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-03
check problems were not corrected in time Errors in '\donttest' parts of examples
1.0.1
2019-05-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-04
Total releases: 12 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Download size: 3.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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