R Observatory: Metrics for babelgene version 22.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

babelgene

22.9

Gene Orthologs for Model Organisms in a Tidy Data Format

1packages depend

185.3Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Igor DolgalevFirst published 2021-04-263 releasesCRAN page ↗GitHub ↗

Genomic analysis of model organisms frequently requires the use of databases based on human data or making comparisons to patient-derived resources. This requires harmonization of gene names into the same gene space. The 'babelgene' R package converts between human and non-human gene orthologs/homologs. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 doi:10.1007/s00335-005-0103-2, Eyre et al. 2007 doi:10.1093/bib/bbl030, Seal et al. 2011 doi:10.1093/nar/gkq892).

Install

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

install.packages("babelgene", 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("igordot/babelgene")

Development version from igordot/babelgene. 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-babelgene

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-babelgene

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-babelgene

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

Health

CRAN checks

13OK

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.26

100.0%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 114 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

185.3K

CRAN downloads in the past year

Rank #831 · ~508/day · ~15.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

19.4K30 days

57.4K90 days

185.3K1 year

Compare downloads with other packages →

Also on1.2K r2u63 autocran14.6K conda_forge29 c2d4u

Repository

GitHub ↗ igordot/babelgene

16Stars

5Forks

1Open issues

0Open PRs

3Releases

31Commits

1Contributors

31 commits · Last activity 2022-09-29 · 0% stars, 30d

Stars over time

2025-07-24 · 142026-07-07 · 16

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/igordot/babelgene on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4

Imports (3)

dplyrmethodsrlang

LinkingTo (0)

none

Suggests (4)

covr knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

4indirect

msigdbr

Code & Tests

People & History

People (1)

Maintainer (1)

Igor Dolgalev

Author, Maintainer

Authors (1)

Igor Dolgalev

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. 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
22.9Latest
2022-09-29 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
22.3
2022-03-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
21.4
2021-04-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-26
Total releases: 3 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4
Download size: 3.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("babelgene")

Format

Dolgalev, I. (2022). babelgene: Gene Orthologs for Model Organisms in a Tidy Data Format (Version 22.9) [Computer software]. https://doi.org/10.32614/CRAN.package.babelgene

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for babelgene version 22.9 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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