Package: DMRcate
Title: Methylation array and sequencing spatial analysis methods
Version: 3.5.2
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: 2025-08-31 20:18:54 UTC; biocbuild
Maintainer: Tim Peters <t.peters@garvan.org.au>
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: devel
git_last_commit: 607fe30
git_last_commit_date: 2025-08-31
Repository: Bioconductor 3.22
Date/Publication: 2025-08-31
Built: R 4.5.1; ; 2025-09-01 02:32:38 UTC; unix
