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

DOI: 10.18129/B9.bioc.DMRcaller    

Differentially Methylated Regions caller

Bioconductor version: Release (3.5)

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 R Script DMRcaller
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
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_1.8.0.tar.gz
Windows Binary DMRcaller_1.8.0.zip
Mac OS X 10.11 (El Capitan) DMRcaller_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DMRcaller
Package Short Url http://bioconductor.org/packages/DMRcaller/
Package Downloads Report Download Stats

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