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DMRcaller

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

Differentially Methylated Regions caller


Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version 1.35.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
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Suggests knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package DMRcaller_1.35.0.tar.gz
Windows Binary
macOS Binary (x86_64) DMRcaller_1.35.0.tgz
macOS Binary (arm64)
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