methylKit
Bioc currentDNA methylation analysis from high-throughput bisulfite sequencing results
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
130 23 exported
Complexity
3.6 avg / 21 max
Call network
130 nodes / 123 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
23,582
Files
144
Compiled share
6.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
57
Internal functions
90
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
5.6%
Unsafe pattern score
0
Dep constraint coverage
13%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
1 externalGNU make
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 53
- Examples that run
- 96%44 run in a plain check · 2 never run
- Exported functions with examples
- 93%
- Documented parameters
- 98%
- Return-value docs
- 85%
- Help pages citing references
- 6%
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/al2na/methylkit on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bismark_cytosineReport | data.frame | 28 × 7 | No other package |
| control1.myCpG | data.frame | 2,377 × 7 | No other package |
| control2.myCpG | data.frame | 1,697 × 7 | No other package |
| cpgi.hg18.bed | data.frame | 1,894 × 4 | No other package |
| ctrl1.txt | – | – | – |
| ctrl2.txt | data.frame | 1,696 × 7 | No other package |
| generic1.CpG | data.frame | 6 × 6 | No other package |
| methylBase.obj | methylBase | 16 elements | No other package |
| methylDiff.obj | methylDiff | 7 elements | No other package |
| methylRawList.obj | methylRawList | 4 elements | No other package |
| refseq.hg18.bed | – | – | – |
| test1.myCpG | data.frame | 1,904 × 7 | No other package |
| test1.txt | data.frame | 1,843 × 7 | No other package |
| test1_test2_ctrl1_ctrl2.txt | data.frame | 962 × 16 | No other package |
| test1_test2_ctrl1_ctrl2_diffMeth.txt | data.frame | 910 × 7 | No other package |
| test2.myCpG | data.frame | 2,006 × 7 | No other package |
| test2.txt | – | – | – |
Topics
Depended on by (4)
Bioconductor (4)
Suggested by (1)
People (from the free-text Author field)
- Altuna Akalin author maintainer
- Matthias Kormaksson author
- Sheng Li author
- Arsene Wabo contributor
- Adrian Bierling author
- Alexander Blume author
- Katarzyna Wreczycka contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("methylKit")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 v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.