DMRcate

Methylation array and sequencing spatial analysis methods

Bioconductor version: 3.23 · Package version: 3.8.0

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.

Installation

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

BiocManager::install("DMRcate")

Details

Maintainer	Tim Peters <t.peters@garvan.org.au>
Author	Tim Peters
License	file LICENSE
Downloads rank	1569
Source branch	RELEASE_3_23
biocViews	Coverage, DNAMethylation, DataImport, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, Genetics, GenomeAnnotation, MethylationArray, Microarray, MultipleComparison, OneChannel, Preprocessing, QualityControl, Sequencing, Software, TimeCourse, TwoChannel, WholeGenome

Download

Follow the 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 (arm64)	DMRcate_3.8.0.tgz
macOS binary (x86_64)	DMRcate_3.8.0.tgz

Dependencies

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

Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest

Reverse dependencies

Depends On Me (2): ChAMP, methylationArrayAnalysis

Suggests Me (2): easyEWAS, missMethyl