geneset

0.2.7

Get Gene Sets for Gene Enrichment Analysis

1packages depend

5.3Kdownloads / year

14.0%test coverage

13/13checks pass

Overview

About

Maintained by Yunze LiuFirst published 2022-07-182 releasesCRAN page ↗GitHub ↗

Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) doi:10.1093/nar/gkh036), 'KEGG' (Minoru et al. (2000) doi:10.1093/nar/28.1.27), 'WikiPathway' (Marvin et al. (2020) doi:10.1093/nar/gkaa1024), 'MsigDb' (Arthur et al. (2015) doi:10.1016/j.cels.2015.12.004), 'Reactome' (David et al. (2011) doi:10.1093/nar/gkq1018), 'MeSH' (Ish et al. (2014) doi:10.4103/0019-5413.139827), 'DisGeNET' (Janet et al. (2017) doi:10.1093/nar/gkw943), 'Disease Ontology' (Lynn et al. (2011) doi:10.1093/nar/gkr972), 'Network of Cancer Genes' (Dimitra et al. (2019) doi:10.1186/s13059-018-1612-0) and 'COVID-19' (Maxim et al. (2020) doi:10.21203/rs.3.rs-28582/v1). Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'. The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of terms ID and term description.

Install

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

install.packages("geneset", 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("GangLiLab/geneset")

Development version from GangLiLab/geneset. 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-geneset

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

# 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-geneset

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

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Check history

OK2026-06-01
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-31
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-21
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-31
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

5.3K

CRAN downloads in the past year

Rank #9,144 · ~15/day · ~442/mo

geneset Releases R versions

Daily download trend is not available in this view yet.

34330 days

1.2K90 days

5.3K1 year

Compare downloads with other packages →

Also on94 r2u31 autocran142 conda_forge

Repository

GitHub ↗ ganglilab/geneset

11Stars

1Forks

1Open issues

0Open PRs

0Releases

33Commits

1Contributors

enrichment-analysisgenegeneset-enrichment

License GPL-3.0 · 33 commits · Last activity 2023-08-09 · +10% stars, 30d

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ganglilab/geneset on 2026-07-19.

Lint, format, editor (1)

RStudio project

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 (5)

dplyr RCurl fst stringi stringr

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

genekitr

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Yunze Liu

Author, Maintainer

Authors (1)

Yunze Liu

Author, Maintainer

Package Timeline

2 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.7Latest
2022-11-20 · current release · diff ↗
unarchivedReturned to CRAN
2022-11-20
archivedRemoved from CRAN
2022-11-11
policy violation On Internet access
0.2.6
2022-07-18
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-18
Total releases: 2 / 4 yrs
License: GPL-3 OSI
Download size: 206 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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