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

Methylation array and sequencing spatial analysis methods

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome
Version 3.1.2
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License file LICENSE
Depends R (>= 4.3.0)
Imports AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices
System Requirements
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Suggests knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
Linking To
Depends On Me methylationArrayAnalysis
Imports Me
Suggests Me missMethyl
Links To Me
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Source Package DMRcate_3.1.2.tar.gz
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macOS Binary (x86_64) DMRcate_3.1.4.tgz
macOS Binary (arm64) DMRcate_3.1.1.tgz
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