Bioconductor release scheduled for October 29

DMRcaller

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

Differentially Methylated Regions Caller


Bioconductor version: Development (3.22)

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")):

Installation

To install this package, start R (version "4.5") 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")
Overview of the DMRcaller package HTML R Script
Reference Manual PDF

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version 1.41.2
In Bioconductor since BioC 3.1 (R-3.2) (10.5 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
System Requirements
URL
See More
Suggests knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38
Linking To
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Depends On Me
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Package Archives

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

Source Package DMRcaller_1.41.2.tar.gz
Windows Binary (x86_64) DMRcaller_1.41.1.zip
macOS Binary (x86_64) DMRcaller_1.41.2.tgz
macOS Binary (arm64) DMRcaller_1.41.2.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