DOI: 10.18129/B9.bioc.methylKit    

This is the development version of methylKit; for the stable release version, see methylKit.

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: Development (3.7)

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. Perl is needed to read SAM files only.

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

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

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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


biocViews DNAMethylation, MethylSeq, Sequencing, Software
Version 1.5.2
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License Artistic-2.0
Depends R (>= 3.3.0), 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, Rcpp, R.utils, limma, grDevices, graphics, stats, utils
LinkingTo Rcpp, Rhtslib, zlibbioc
Suggests testthat, knitr, rmarkdown, genomation
Depends On Me
Imports Me methInheritSim, methylInheritance
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methylKit_1.5.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) methylKit_1.5.2.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: