Package: minfi
Version: 1.56.0
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 (>= 1.61.1),
        SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2),
        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, Seqinfo, 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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:09:18 UTC
RemoteUrl: https://github.com/bioc/minfi
RemoteRef: RELEASE_3_22
RemoteSha: e6780b44c4c4ab38bee5f31d43c87513820059b1
NeedsCompilation: no
Packaged: 2025-11-16 07:46:30 UTC; root
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 4.5.2; ; 2025-11-16 07:53:25 UTC; windows
