methylKit
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methylKit.
DNA methylation analysis from high-throughput bisulfite sequencing results
Bioconductor version: 3.9
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("methylKit")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, MethylSeq, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils |
| System Requirements | |
| URL | http://code.google.com/p/methylkit/ |
See More
| Suggests | testthat, knitr, rmarkdown, genomation, BiocManager |
| Linking To | Rcpp, Rhtslib(>= 1.13.1), zlibbioc |
| Enhances | |
| Depends On Me | |
| Imports Me | 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_1.10.0.tar.gz |
| Windows Binary | methylKit_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | methylKit_1.10.0.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 3.9 | Source Archive |