bsseq
Bioc currentAnalyze, manage and store whole-genome methylation data
Release Lineage
Entered 2.11 · Oct 3, 2012
Current · Requires R 4.6
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.
None published for Bioconductor
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 →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
10,765
Files
97
Compiled share
1.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
31
Internal functions
81
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
–
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 externalC++17
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
- Help pages
- 29 (4 internal)
- Examples that run
- 84%21 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
- Exported functions with examples
- 90%
- Documented parameters
- 100%
- Return-value docs
- 81%
- Help pages citing references
- 17%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/kasperdanielhansen/bsseq on 2026-10-11.
The R CMD check workflow runs on Linux and macOS, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| BS.chr22 | – | – | – |
| Hypo1.first50Bed | data.frame | 49 × 18 | No other package |
Topics
Depended on by (17)
Show all 21 packagesHide all 21 packages
Bioconductor (17)
Suggested by (4)
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' entry:
citation("bsseq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/gb-2012-13-10-r83.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.