orthogene
Bioc currentGene mapping made easy
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
96 14 exported
Complexity
4.3 avg / 25 max
Call network
96 nodes / 220 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
9,902
Files
200
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
82
Testing
Has tests
Yes
Test-to-code ratio
0.18
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2022-04-08
Latest release
2026-04-29
Avg cadence
177 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 45 (26 internal)includes a package overview page
- Examples that run
- 100%14 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- docker HTML
- Infer species HTML
- orthogene HTML
Bug fixes
test-map_genes: replacemessage(e)withmessage(conditionMessage(e))in the planarian (Schmidtea mediterranea) tryCatch error handler. Same pattern as the 1.17.4 fix torun_benchmark_once(): passing a condition object tomessage()re-signals it, and under testthat's calling handlers an error condition signaled this way escapes thetryCatchand is reported as a test failure. This causedtest-map_genesto fail on the GitHub Actions Windows runner whenever the planosphere mapping file failed to download.
From NEWS.md in the release
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/neurogenomics/orthogene on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-04-29
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| exp_mouse | dgCMatrix | 15,259 × 7 | No other package |
| exp_mouse_enst | dgeMatrix | 482 × 7 | No other package |
| gprofiler_namespace | – | – | – |
1 internal object is bundled for the package's own use and not listed here.
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (1)
People
- Brian Schilder maintainer funder
Cite
Cite this package
Run in R for the authors' entry:
citation("orthogene")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.64898/2026.01.17.700094.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.