methylKit

DOI: 10.18129/B9.bioc.methylKit    

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: Release (3.8)

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

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("methylKit", version = "3.8")

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 1.8.1
In Bioconductor since BioC 3.4 (R-3.3) (2 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(>= 1.13.1), zlibbioc
Suggests testthat, knitr, rmarkdown, genomation, BiocManager
SystemRequirements
Enhances
URL http://code.google.com/p/methylkit/
Depends On Me
Imports Me 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_1.8.1.tar.gz
Windows Binary methylKit_1.8.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) methylKit_1.8.1.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 http://bioconductor.org/packages/methylKit/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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