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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("methylKit")
In most cases, you don't need to download the package archive at all.
methylKit
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see methylKit.
DNA methylation analysis from high-throughput bisulfite sequencing results
Bioconductor version: 3.4
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>
Citation (from within R,
enter citation("methylKit")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("methylKit")
Documentation
| HTML | R Script | Vignette Title |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, MethylSeq, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.0), GenomicRanges(>= 1.18.1), methods |
| Imports | IRanges, data.table (>= 1.9.6), parallel, S4Vectors, GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, Rcpp, R.utils, limma, grDevices, graphics, stats, utils |
| LinkingTo | Rcpp, Rhtslib, zlibbioc |
| Suggests | testthat, knitr, rmarkdown, genomation |
| SystemRequirements | |
| Enhances | |
| URL | http://code.google.com/p/methylkit/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | methylKit_1.0.0.tar.gz |
| Windows Binary | methylKit_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | methylKit_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/methylKit/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/methylKit/ |
| Package Downloads Report | Download Stats |
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