methylKit

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 gmail.com>, Alexander Blume <alex.gos90 at gmail.com>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

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
URL	https://github.com/al2na/methylKit
Bug Reports	https://github.com/al2na/methylKit/issues

Suggests	testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
Linking To	Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Enhances
Depends On Me
Imports Me	deconvR, 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_1.30.0.tar.gz
Windows Binary (x86_64)	methylKit_1.30.0.zip (64-bit only)
macOS Binary (x86_64)	methylKit_1.30.0.tgz
macOS Binary (arm64)	methylKit_1.30.0.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