DMRcaller

Differentially Methylated Regions caller

Bioconductor version: Release (3.20)

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 (version "4.4") and enter:


if (!require("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")

DMRcaller	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 years)
License	GPL-3
Depends	R (>= 3.5), GenomicRanges, IRanges, S4Vectors(>= 0.23.10)
Imports	parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils
System Requirements
URL

Suggests	knitr, RUnit, BiocGenerics
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Build Report	Build Report

Package Archives

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

Source Package	DMRcaller_1.38.0.tar.gz
Windows Binary (x86_64)	DMRcaller_1.38.0.zip
macOS Binary (x86_64)	DMRcaller_1.38.0.tgz
macOS Binary (arm64)	DMRcaller_1.37.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMRcaller
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DMRcaller
Bioc Package Browser	https://code.bioconductor.org/browse/DMRcaller/
Package Short Url	https://bioconductor.org/packages/DMRcaller/
Package Downloads Report	Download Stats