DMRcaller
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DMRcaller.
Differentially Methylated Regions caller
Bioconductor version: 3.9
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 "3.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), GenomicRanges, IRanges, S4Vectors |
| 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_1.16.0.tar.gz |
| Windows Binary | DMRcaller_1.16.0.zip |
| Mac OS X 10.11 (El Capitan) | DMRcaller_1.16.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |