methylKit

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see methylKit.

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: 3.15

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 "4.2") 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 1.22.0

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/

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

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