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("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 | ||
| NEWS | Text |
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 | |
| 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_1.41.2.tar.gz |
| Windows Binary (x86_64) | DMRcaller_1.41.1.zip (64-bit only) |
| 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 |