R Observatory: Metrics for BSgenome version 1.80.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BSgenome

Bioc current

Software infrastructure for efficient representation of full genomes and their SNPs

v1.80.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 1.9 · Oct 4, 2006

Current · Requires R 4.6

1.0 In 40 of 49 releases 3.23

Description

Infrastructure shared by all the Biostrings-based genome data packages.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

190 34 exported

Complexity

3.4 avg / 13 max

Call network

190 nodes / 222 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

9,138

Files

41

Compiled share

0%

Has compiled src

No

Language breakdown

R 5,955 (65.2%)Docs 2,328 (25.5%)Vignettes 855 (9.4%)

API

Exported functions

51

Internal functions

149

Recent export changes

v3.5+13 saveAsOnDiskLongTable_old, saveRowidsForOnDiskLongTable_old, OnDiskLongTable_old +10 more −3 saveAsOnDiskLongTable, saveRowidsForOnDiskLongTable, getRowsByIndexFromOnDiskLongTable

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

62.7%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

50%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

2.8.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

40

First release

2006-10-07

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

16

LOC over versions

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

Documentation

READMEYes · 45 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 56%
References docs: 0%

Topics

Software › ResearchField › Genetics

Software › Infrastructure

Software › Infrastructure › DataRepresentation

Software › BiologicalQuestion › SequenceMatching

Software › WorkflowStep › Annotation

Software › AssayDomain › SNP

Depended on by (308)

CRAN (8)

ActiveDriverWGS GencoDymo2 TmCalculator revert Signac gkmSVM polyRAD sigminer

People

Hervé Pagès author maintainer

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BSgenome")

Format

Pagès, H. (2026). BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs (Version 1.80.0) [Computer software]. https://bioconductor.org/packages/BSgenome

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 BSgenome version 1.80.0 [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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