DMRcaller
Differentially Methylated Regions Caller
Bioconductor version: 3.24 · Package version: 1.45.3
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DMRcaller")Details
| Maintainer | Nicolae Radu Zabet <r.zabet@qmul.ac.uk> |
| Author | Nicolae Radu Zabet <r.zabet@qmul.ac.uk>, Jonathan Michael Foonlan Tsang <jmft2@cam.ac.uk>, Alessandro Pio Greco <apgrec@essex.ac.uk>, Ryan Merritt <rmerri@essex.ac.uk> and Young Jun Kim <qc25039@qmul.ac.uk> |
| License | GPL-3 |
| Downloads rank | 666 |
| Source branch | devel |
| biocViews | Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | DMRcaller_1.45.3.tar.gz |
| Windows binary (x86_64) | DMRcaller_1.45.3.zip |
| macOS binary (arm64) | DMRcaller_1.45.3.tgz |
| macOS binary (x86_64) | DMRcaller_1.45.3.tgz |
Dependencies
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, cigarillo
Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38