methylSig
Bioc currentMethylSig: Differential Methylation Testing for WGBS and RRBS Data
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 9 exported
Complexity
9.5 avg / 38 max
Call network
13 nodes / 3 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
3,918
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
4
Testing
Has tests
Yes
Test-to-code ratio
1.07
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-04-27
Latest release
2026-09-26
Avg cadence
183 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14 (1 internal)includes a package overview page
- Examples that run
- 100%13 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Updating methylSig code HTML
- Using methylSig HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/sartorlab/methylsig on 2026-10-11.
The R CMD check workflow runs on Linux, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bsseq_destranded | – | – | – |
| bsseq_multichrom | – | – | – |
| bsseq_stranded | – | – | – |
| promoters_gr | – | – | – |
24 internal objects are bundled for the package's own use and not listed here.
Topics
People
- Raymond G. Cavalcante author maintainer
- Yongseok Park author
Cite
Cite this package
Run in R for the authors' entry:
citation("methylSig")The package provides a citation file, so citation() returns the authors' own entry.
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.