DMRcaller

DOI: 10.18129/B9.bioc.DMRcaller    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DMRcaller.

Differentially Methylated Regions caller

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DMRcaller")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4.5 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_1.16.0.tar.gz
Windows Binary	DMRcaller_1.16.0.zip
Mac OS X 10.11 (El Capitan)	DMRcaller_1.16.0.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	https://bioconductor.org/packages/DMRcaller/
Package Downloads Report	Download Stats