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DMRcaller

Differentially Methylated Regions caller

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version 1.32.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, IRanges, S4Vectors(>= 0.23.10)
Imports parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils
Linking To
Suggests knitr, RUnit, BiocGenerics
System Requirements
Enhances
URL
See More
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_1.32.0.tar.gz
Windows Binary DMRcaller_1.32.0.zip
macOS Binary (x86_64) DMRcaller_1.32.0.tgz
macOS Binary (arm64) DMRcaller_1.32.0.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