methylKit

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see methylKit.

DNA methylation analysis from high-throughput bisulfite sequencing results


Bioconductor version: 3.14

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 Gosdschan [aut]

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

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylKit")

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

Documentation

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

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

Details

biocViews DNAMethylation, MethylSeq, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
URL http://code.google.com/p/methylkit/
See More
Suggests testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
Linking To Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Enhances
Depends On Me
Imports Me deconvR, MethCP, methInheritSim, methylInheritance
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package methylKit_1.20.0.tar.gz
Windows Binary methylKit_1.20.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) methylKit_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/methylKit
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methylKit
Bioc Package Browser https://code.bioconductor.org/browse/methylKit/
Package Short Url https://bioconductor.org/packages/methylKit/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive