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DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: Release (3.19)

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.

Author: Altuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Blume [aut], Katarzyna Wreczycka [ctb]

Maintainer: Altuna Akalin <aakalin at>, Alexander Blume <alex.gos90 at>

Citation (from within R, enter citation("methylKit")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

methylKit: User Guide v`r packageVersion('methylKit')` HTML R Script
Reference Manual PDF


biocViews DNAMethylation, MethylSeq, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (8 years)
License Artistic-2.0
Depends R (>= 3.5.0), GenomicRanges(>= 1.18.1), methods
Imports IRanges, data.table (>= 1.9.6), parallel, S4Vectors(>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils
System Requirements GNU make
Bug Reports
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Suggests testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Depends On Me
Imports Me deconvR, methInheritSim, methylInheritance
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package methylKit_1.30.0.tar.gz
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macOS Binary (x86_64) methylKit_1.30.0.tgz
macOS Binary (arm64) methylKit_1.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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