R Observatory: Metrics for GenomeInfoDb version 1.48.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenomeInfoDb

Bioc current

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

v1.48.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.14 · Apr 14, 2014

Current · Requires R 4.6

1.0 In 25 of 49 releases 3.23

Description

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

166 25 exported

Complexity

4 avg / 25 max

Call network

166 nodes / 252 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

7,037

Files

254

Compiled share

0%

Has compiled src

No

Language breakdown

R 5,090 (72.3%)Tests 2 (0%)Docs 1,579 (22.4%)Vignettes 366 (5.2%)

API

Exported functions

52

Internal functions

133

Recent export changes

v3.8+1 checkCompatibleSeqinfo

v3.7+1 loadTaxonomyDb

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

61.5%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

16.7%

Unsafe pattern score

0

Dep constraint coverage

50%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

25

First release

2014-04-14

Latest release

2026-04-28

Avg cadence

166 days

Cold removal rate

100%

Dep drift

14

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 47 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 80%
References docs: 10%

Topics

Software › ResearchField › Genetics

Software › Infrastructure › DataRepresentation

Software › WorkflowStep › Annotation

Software › BiologicalQuestion › GenomeAnnotation

Depended on by (366)

CRAN (19)

ActiveDriverWGS DESNP Signac TmCalculator crispRdesignR driveR hicream karyotapR locuszoomr ocrRBBR revert tepr CNVScope GRIN2 RapidoPGS Seurat gkmSVM gwas2crispr polyRAD

People

Hervé Pagès author maintainer
Sonali Arora author
Marc Carlson author
Emmanuel Chigozie Elendu contributor
Atuhurira Kirabo Kakopo contributor
Haleema Khan contributor
Prisca Chidimma Maduka contributor
Martin Morgan author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GenomeInfoDb")

Format

Pagès, H., Arora, S., Carlson, M., Elendu, E. C., Kakopo, A. K., Khan, H., Maduka, P. C., & Morgan, M. (2026). GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style (Version 1.48.0) [Computer software]. https://bioconductor.org/packages/GenomeInfoDb

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 GenomeInfoDb version 1.48.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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