methylKit

DOI: 10.18129/B9.bioc.methylKit    

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DNAMethylation, MethylSeq, Sequencing, Software
Version	1.14.2
In Bioconductor since	BioC 3.4 (R-3.3) (4 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
LinkingTo	Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Suggests	testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
SystemRequirements	GNU make
Enhances
URL	http://code.google.com/p/methylkit/
Depends On Me
Imports Me	MethCP, methInheritSim, methylInheritance
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	methylKit_1.14.2.tar.gz
Windows Binary	methylKit_1.14.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	methylKit_1.14.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylKit
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylKit
Package Short Url	https://bioconductor.org/packages/methylKit/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive