DMRcate

DOI: 10.18129/B9.bioc.DMRcate  

This is the development version of DMRcate; for the stable release version, see DMRcate.

Methylation array and sequencing spatial analysis methods

Bioconductor version: Development (3.18)

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Author: Tim Peters

Maintainer: Tim Peters <t.peters at garvan.org.au>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DMRcate")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version	2.15.0
In Bioconductor since	BioC 2.14 (R-3.1) (9.5 years)
License	file LICENSE
Depends	R (>= 4.0.0)
Imports	ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment
LinkingTo
Suggests	knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata
SystemRequirements
Enhances
URL
Depends On Me	ChAMP, methylationArrayAnalysis
Imports Me
Suggests Me	missMethyl
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary	DMRcate_2.15.0.zip
macOS Binary (x86_64)	DMRcate_2.15.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/DMRcate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DMRcate
Bioc Package Browser	https://code.bioconductor.org/browse/DMRcate/
Package Short Url	https://bioconductor.org/packages/DMRcate/
Package Downloads Report	Download Stats