Package: DMRcate
Title: Methylation array and sequencing spatial analysis methods
Version: 2.14.0
Date: 2022-07-02
Author: Tim Peters
Maintainer: Tim Peters <t.peters@garvan.org.au>
Authors@R: c(person("Tim", "Peters", role = c("cre", "aut"),
                    email = "t.peters@garvan.org.au"),
	     person("Mike", "Buckley", role = "aut"),
             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 (>= 4.0.0)
Imports: ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, minfi,
        missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils,
        S4Vectors, methods, graphics, SummarizedExperiment
biocViews: DifferentialMethylation, GeneExpression, Microarray,
        MethylationArray, Genetics, DifferentialExpression,
        GenomeAnnotation, DNAMethylation, OneChannel, TwoChannel,
        MultipleComparison, QualityControl, TimeCourse, Sequencing,
        WholeGenome, Epigenetics, Coverage, Preprocessing, DataImport
Suggests: knitr, RUnit, BiocGenerics,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
        FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata
License: file LICENSE
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DMRcate
git_branch: RELEASE_3_17
git_last_commit: 6e7bae0
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-30
NeedsCompilation: no
Packaged: 2023-04-30 22:55:48 UTC; biocbuild
Built: R 4.3.0; ; 2023-05-01 12:06:52 UTC; windows
