DMRcaller

Differentially Methylated Regions Caller

Bioconductor version: 3.23 · Package version: 1.44.0

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	439
Source branch	RELEASE_3_23
biocViews	Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software

Documentation

Overview of the DMRcaller package

Download

Source package

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

Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38