R Observatory: Metrics for VariantAnnotation version 1.58.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VariantAnnotation

Bioc current

Annotation of Genetic Variants

v1.58.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.9 · Nov 1, 2011

Current · Requires R 4.6

1.0 In 30 of 49 releases 3.23

Description

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

210 44 exported

Complexity

3.2 avg / 26 max

Call network

210 nodes / 178 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

13,630

Files

136

Compiled share

11.9%

Has compiled src

Yes

Language breakdown

R 6,005 (44.1%)C/C++/src 1,616 (11.9%)Tests 2 (0%)Docs 4,854 (35.6%)Vignettes 1,153 (8.5%)

API

Exported functions

80

Internal functions

105

Recent export changes

v3.9−1 restrictToSNV

v3.5+2 idType, idType<-

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

97.5%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

100%

Unsafe pattern score

0

Dep constraint coverage

63.2%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

1

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

30

First release

2011-11-16

Latest release

2026-04-28

Avg cadence

183 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

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 40%
References docs: 26%

Topics

Software › Infrastructure › DataImport

Software › Technology › Sequencing

Software › AssayDomain › SNP

Software › WorkflowStep › Annotation

Software › ResearchField › Genetics

Software › BiologicalQuestion › VariantAnnotation

Depended on by (136)

CRAN (7)

PlasmaMutationDetector gpcp MoBPS SNPassoc ldsep polyRAD updog

People

Bioconductor Package Maintainer maintainer
Stephanie Gogarten contributor
Michael Lawrence author
Martin Morgan author
Valerie Oberchain author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VariantAnnotation")

Format

Bioconductor Package Maintainer, Gogarten, S., Lawrence, M., Morgan, M., & Oberchain, V. (2026). VariantAnnotation: Annotation of Genetic Variants (Version 1.58.0) [Computer software]. https://bioconductor.org/packages/VariantAnnotation

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 VariantAnnotation version 1.58.0 [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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