R Observatory: Metrics for bsseq version 1.48.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bsseq

Bioc current

Analyze, manage and store whole-genome methylation data

v1.48.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.11 · Oct 3, 2012

Current · Requires R 4.6

1.0 In 28 of 49 releases 3.23

Description

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

116 31 exported

Complexity

6.2 avg / 31 max

Call network

116 nodes / 129 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

10,765

Files

103

Compiled share

1.5%

Has compiled src

Yes

Language breakdown

R 5,330 (49.5%)C/C++/src 158 (1.5%)Tests 817 (7.6%)Docs 2,476 (23%)Vignettes 1,984 (18.4%)

API

Exported functions

31

Internal functions

81

Recent export changes

v3.8+1 findLoci

Testing & CI

Has tests

Yes

Test-to-code ratio

0.15

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

93.5%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

100%

Unsafe pattern score

0

Dep constraint coverage

34.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0

System requirements

1

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

28

First release

2012-10-16

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

24

LOC over versions

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

Documentation

READMEYes · 17 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 84%
Documented parameters: 100%
Return-value docs: 81%
References docs: 17%

Topics

Software › AssayDomain › DNAMethylation

Depended on by (21)

CRAN (1)

methFuse

People

Kasper Daniel Hansen author maintainer
Peter Hickey author
Aaron Lun contributor
Hervé Pagès contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bsseq")

Format

Hansen, K. D., Hickey, P., Lun, A., & Pagès, H. (2026). bsseq: Analyze, manage and store whole-genome methylation data (Version 1.48.0) [Computer software]. https://bioconductor.org/packages/bsseq

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 bsseq 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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