DMRcaller

DOI: 10.18129/B9.bioc.DMRcaller    

Differentially Methylated Regions caller

Bioconductor version: Release (3.6)

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>

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	1.10.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 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.

Source Package	DMRcaller_1.10.0.tar.gz
Windows Binary	DMRcaller_1.10.0.zip
Mac OS X 10.11 (El Capitan)	DMRcaller_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMRcaller
Package Short Url	http://bioconductor.org/packages/DMRcaller/
Package Downloads Report	Download Stats