Package: minfi
Version: 1.50.0
Title: Analyze Illumina Infinium DNA methylation arrays
Description: Tools to analyze & visualize Illumina Infinium methylation arrays.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
                    email = "kasperdanielhansen@gmail.com"),
             person("Martin", "Aryee", role = "aut"),
             person(c("Rafael", "A."), "Irizarry", role = "aut"),
             person(c("Andrew", "E."), "Jaffe", role = "ctb"),
             person("Jovana", "Maksimovic", role = "ctb"),
             person(c("E.", "Andres"), "Houseman", role = "ctb"),
             person("Jean-Philippe", "Fortin", role = "ctb"),
             person("Tim", "Triche", role = "ctb"),
             person(c("Shan", "V."), "Andrews", role = "ctb"),
             person(c("Peter", "F."), "Hickey", role = "ctb"))
Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges,
        SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>=
        1.1.9)
Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0),
        IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
        minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>=
        1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools
Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges,
        beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma,
        preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>=
        1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog,
        data.table, GEOquery, stats, grDevices, graphics, utils,
        DelayedArray (>= 0.15.16), HDF5Array, BiocParallel
Collate: AllGenerics.R MethylSet-class.R RatioSet-class.R
        RGChannelSet-class.R RGChannelSetExtended-class.R
        GenomicMethylSet-class.R GenomicRatioSet-class.R eSet_methods.R
        utils.R IlluminaMethylationManifest-class.R
        IlluminaMethylationAnnotation-class.R minfiQC.R getSex.R
        dmpFinder.R blocks.R plot.R plotBetasByType.R preprocessRaw.R
        preprocessIllumina.R detectionP.R preprocessSwan.R
        preprocessQuantile.R preprocessNoob.R preprocessFunnorm.R qc.R
        read.450k.R read.meth.R read.meth2.R read.geo.R read.manifest.R
        bumphunter.R estimateCellCounts.R gaphunter.R compartments.R
        combineArrays.R DelayedArray_utils.R
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/hansenlab/minfi
BugReports: https://github.com/hansenlab/minfi/issues
biocViews: ImmunoOncology, DNAMethylation, DifferentialMethylation,
        Epigenetics, Microarray, MethylationArray, MultiChannel,
        TwoChannel, DataImport, Normalization, Preprocessing,
        QualityControl
git_url: https://git.bioconductor.org/packages/minfi
git_branch: RELEASE_3_19
git_last_commit: 8f33a8b
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-02 00:05:13 UTC; biocbuild
Author: Kasper Daniel Hansen [cre, aut],
  Martin Aryee [aut],
  Rafael A. Irizarry [aut],
  Andrew E. Jaffe [ctb],
  Jovana Maksimovic [ctb],
  E. Andres Houseman [ctb],
  Jean-Philippe Fortin [ctb],
  Tim Triche [ctb],
  Shan V. Andrews [ctb],
  Peter F. Hickey [ctb]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Built: R 4.4.0; ; 2024-05-02 13:06:50 UTC; windows
