DMRcaller
Differentially Methylated Regions caller
Bioconductor version: Release (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("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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software |
Version | 1.36.0 |
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 |
See More
Suggests | knitr, RUnit, BiocGenerics |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | DMRcaller_1.36.0.tar.gz |
Windows Binary | DMRcaller_1.36.0.zip (64-bit only) |
macOS Binary (x86_64) | DMRcaller_1.36.0.tgz |
macOS Binary (arm64) | DMRcaller_1.36.0.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 |