DMRcaller

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Differentially Methylated Regions Caller

Bioconductor version: Development (3.24)

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 <r.zabet at qmul.ac.uk>, Jonathan Michael Foonlan Tsang <jmft2 at cam.ac.uk>, Alessandro Pio Greco <apgrec at essex.ac.uk>, Ryan Merritt <rmerri at essex.ac.uk> and Young Jun Kim <qc25039 at qmul.ac.uk>

Maintainer: Nicolae Radu Zabet <r.zabet at qmul.ac.uk>

Citation (from within R, enter citation("DMRcaller")):

Nicolae Radu Zabet, Jonathan Michael Foonlan Tsang, Alessandro Pio Greco, Ryan Merritt and Young Jun Kim. DMRcaller: Differentially Methylated Regions Caller. doi:10.18129/B9.bioc.DMRcaller, R package version 1.45.3, https://bioconductor.org/packages/DMRcaller.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

Overview of the DMRcaller package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version	1.45.3
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-3
Depends	R (>= 3.5), GenomicRanges, IRanges, S4Vectors
Imports	parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils, Rsamtools, GenomicRanges, GenomicAlignments, Biostrings, BSgenome, BiocManager, S4Vectors, IRanges, InteractionSet, stringr, inflection, BiocParallel, Seqinfo, GenomeInfoDb, cigarillo
System Requirements
URL

Suggests	knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	DMRcaller_1.45.3.tar.gz
Windows Binary (x86_64)	DMRcaller_1.45.3.zip
macOS Binary (big-sur-x86_64)	DMRcaller_1.45.3.tgz
macOS Binary (sonoma-arm64)	DMRcaller_1.45.3.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