To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")

In most cases, you don't need to download the package archive at all.

DMRcaller

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see DMRcaller.

Differentially Methylated Regions caller

Bioconductor version: 3.2

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

Author: Nicolae Radu Zabet <n.r.zabet at gen.cam.ac.uk> and Jonathan Michael Foonlan Tsang <jmft2 at cam.ac.uk>

Maintainer: Nicolae Radu Zabet <n.r.zabet at gen.cam.ac.uk>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DMRcaller")

PDF		DMRcaller
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.1 (R-3.2) (1 year)
License	GPL-3
Depends	R (>= 3.2), GenomicRanges, IRanges, S4Vectors
Imports	parallel, Rcpp, RcppRoll
LinkingTo
Suggests	knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	DMRcaller_1.2.0.tar.gz
Windows Binary	DMRcaller_1.2.0.zip
Mac OS X 10.6 (Snow Leopard)	DMRcaller_1.2.0.tgz
Mac OS X 10.9 (Mavericks)	DMRcaller_1.2.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/DMRcaller/tree/release-3.2
Package Short Url	http://bioconductor.org/packages/DMRcaller/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

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Videos.
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R / CRAN packages and documentation

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