DMRcate

This is the released version of DMRcate; for the devel version, see DMRcate.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Methylation array and sequencing spatial analysis methods

Bioconductor version: Release (3.23)

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>

Citation (from within R, enter citation("DMRcate")):

Tim Peters. DMRcate: Methylation array and sequencing spatial analysis methods. doi:10.18129/B9.bioc.DMRcate, R package version 3.8.0, https://bioconductor.org/packages/DMRcate.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("DMRcate")

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("DMRcate")

DMRcate for EPICv1 and 450K assays	PDF	R Script
DMR calling from EPICv2 arrays	PDF	R Script
DMRcate for bisulfite sequencing assays (WGBS and RRBS)	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version	3.8.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	file LICENSE
Depends	R (>= 4.3.0)
Imports	AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices
System Requirements
URL

Suggests	knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
Linking To
Enhances
Depends On Me	ChAMP, methylationArrayAnalysis
Imports Me
Suggests Me	easyEWAS, missMethyl
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DMRcate_3.8.0.tar.gz
Windows Binary (x86_64)	DMRcate_3.7.0.zip
macOS Binary (big-sur-x86_64)	DMRcate_3.8.0.tgz
macOS Binary (sonoma-arm64)	DMRcate_3.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMRcate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DMRcate
Package Short Url	https://bioconductor.org/packages/DMRcate/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive