DMRcaller

DOI: 10.18129/B9.bioc.DMRcaller    

This is the development version of DMRcaller; for the stable release version, see DMRcaller.

Differentially Methylated Regions caller

Bioconductor version: Development (3.8)

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>, Jonathan Michael Foonlan Tsang <jmft2 at cam.ac.uk>, Alessandro Pio Greco <apgrec at essex.ac.uk> and Ryan Merritt <rmerri at essex.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:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DMRcaller", version = "devel")

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 1.13.8
In Bioconductor since BioC 3.1 (R-3.2) (3.5 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, IRanges, S4Vectors
Imports parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils
LinkingTo
Suggests knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DMRcaller_1.13.8.tar.gz
Windows Binary DMRcaller_1.13.8.zip
Mac OS X 10.11 (El Capitan) DMRcaller_1.13.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/DMRcaller
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DMRcaller
Package Short Url http://bioconductor.org/packages/DMRcaller/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: