DMRcaller
This is the released version of DMRcaller; for the devel version, see DMRcaller.
Differentially Methylated Regions Caller
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Overview of the DMRcaller package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software |
| Version | 1.44.0 |
| 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 |
| 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | DMRcaller_1.44.0.zip |
| macOS Binary (big-sur-x86_64) | DMRcaller_1.44.0.tgz |
| macOS Binary (sonoma-arm64) | DMRcaller_1.44.0.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 |