Package: DMRcate
Title: Methylation array and sequencing spatial analysis methods
Version: 3.9.0
Date: 2025-08-31
Author: Tim Peters
Authors@R: c(person("Tim", "Peters", role = c("cre", "aut"),
                    email = "t.peters@garvan.org.au"),
	     person("Mike", "Buckley", role = "aut"),
	     person("Braydon", "Meyer", role = "ctb"),
             person("Aaron", "Statham", role = "ctb"),
             person("Tim", "Triche, Jr.", role = "ctb"))
Description: 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.
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
biocViews: DifferentialMethylation, GeneExpression, Microarray,
        MethylationArray, Genetics, DifferentialExpression,
        GenomeAnnotation, DNAMethylation, OneChannel, TwoChannel,
        MultipleComparison, QualityControl, TimeCourse, Sequencing,
        WholeGenome, Epigenetics, Coverage, Preprocessing, DataImport
Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38,
        FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
License: file LICENSE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-07-13 09:32:27 UTC; root
Maintainer: Tim Peters <t.peters@garvan.org.au>
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:38:42 UTC
RemoteUrl: https://github.com/bioc/DMRcate
RemoteRef: HEAD
RemoteSha: 120cb6ce3fa01f8968be9030a94b89075da5e20f