{
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  "Package": "minfi",
  "Version": "1.59.1",
  "Title": "Analyze Illumina Infinium DNA methylation arrays",
  "Description": "Tools to analyze & visualize Illumina Infinium methylation\narrays.",
  "Authors@R": "c(person(c(\"Kasper\", \"Daniel\"), \"Hansen\", role = c(\"cre\", \"aut\"),\nemail = \"kasperdanielhansen@gmail.com\"),\nperson(\"Martin\", \"Aryee\", role = \"aut\"),\nperson(c(\"Rafael\", \"A.\"), \"Irizarry\", role = \"aut\"),\nperson(c(\"Andrew\", \"E.\"), \"Jaffe\", role = \"ctb\"),\nperson(\"Jovana\", \"Maksimovic\", role = \"ctb\"),\nperson(c(\"E.\", \"Andres\"), \"Houseman\", role = \"ctb\"),\nperson(\"Jean-Philippe\", \"Fortin\", role = \"ctb\"),\nperson(\"Tim\", \"Triche\", role = \"ctb\"),\nperson(c(\"Shan\", \"V.\"), \"Andrews\", role = \"ctb\"),\nperson(c(\"Peter\", \"F.\"), \"Hickey\", role = \"ctb\"))",
  "Collate": "AllGenerics.R MethylSet-class.R RatioSet-class.R\nRGChannelSet-class.R RGChannelSetExtended-class.R\nGenomicMethylSet-class.R GenomicRatioSet-class.R eSet_methods.R\nutils.R IlluminaMethylationManifest-class.R\nIlluminaMethylationAnnotation-class.R minfiQC.R getSex.R\ndmpFinder.R blocks.R plot.R plotBetasByType.R preprocessRaw.R\npreprocessIllumina.R detectionP.R preprocessSwan.R\npreprocessQuantile.R preprocessNoob.R preprocessFunnorm.R qc.R\nread.450k.R read.meth.R read.meth2.R read.geo.R read.manifest.R\nbumphunter.R estimateCellCounts.R gaphunter.R compartments.R\ncombineArrays.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,\nEpigenetics, Microarray, MethylationArray, MultiChannel,\nTwoChannel, DataImport, Normalization, Preprocessing,\nQualityControl",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-25 23:10:36 UTC",
  "RemoteUrl": "https://github.com/bioc/minfi",
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  "Packaged": {
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  "Author": "Kasper Daniel Hansen [cre, aut],\nMartin Aryee [aut],\nRafael A. Irizarry [aut],\nAndrew E. Jaffe [ctb],\nJovana Maksimovic [ctb],\nE. Andres Houseman [ctb],\nJean-Philippe Fortin [ctb],\nTim Triche [ctb],\nShan V. Andrews [ctb],\nPeter F. Hickey [ctb]",
  "Maintainer": "Kasper Daniel Hansen <kasperdanielhansen@gmail.com>",
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    "getAnnotation",
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    "getProbeInfo",
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      "title": "Analyze Illumina's methylation arrays",
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        "minfi-package",
        "minfi"
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    {
      "page": "blockFinder",
      "title": "Finds blocks of methylation differences for Illumina methylation arrays",
      "topics": [
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    {
      "page": "bumphunter",
      "title": "Methods for function 'bumphunter' in Package 'minfi'",
      "topics": [
        "bumphunter,GenomicRatioSet-method"
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    },
    {
      "page": "combineArrays",
      "title": "A method for combining different types of methylation arrays into a virtual array.",
      "topics": [
        "combineArrays",
        "combineArrays,GenomicMethylSet,GenomicMethylSet-method",
        "combineArrays,GenomicRatioSet,GenomicRatioSet-method",
        "combineArrays,MethylSet,MethylSet-method",
        "combineArrays,RatioSet,RatioSet-method",
        "combineArrays,RGChannelSet,RGChannelSet-method"
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    },
    {
      "page": "compartments",
      "title": "Estimates A/B compartments from Illumina methylation arrays",
      "topics": [
        "compartments",
        "createCorMatrix",
        "extractAB"
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    },
    {
      "page": "controlStripPlot",
      "title": "Plot control probe signals.",
      "topics": [
        "controlStripPlot"
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    },
    {
      "page": "convertArray",
      "title": "A method for converting a type of methylation arrays into a virtual array of another type.",
      "topics": [
        "convertArray",
        "convertArray,GenomicMethylSet-method",
        "convertArray,GenomicRatioSet-method",
        "convertArray,MethylSet-method",
        "convertArray,RatioSet-method",
        "convertArray,RGChannelSet-method"
      ]
    },
    {
      "page": "cpgCollapse",
      "title": "Collapse methylation values of adjacent CpGs into a summary value.",
      "topics": [
        "cpgCollapse"
      ]
    },
    {
      "page": "densityBeanPlot",
      "title": "Density bean plots of methylation Beta values.",
      "topics": [
        "densityBeanPlot"
      ]
    },
    {
      "page": "densityPlot",
      "title": "Density plots of methylation Beta values.",
      "topics": [
        "densityPlot"
      ]
    },
    {
      "page": "detectionP",
      "title": "Detection p-values for all probed genomic positions.",
      "topics": [
        "detectionP"
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    },
    {
      "page": "dmpFinder",
      "title": "Find differentially methylated positions",
      "topics": [
        "dmpFinder"
      ]
    },
    {
      "page": "estimateCellCounts",
      "title": "Cell Proportion Estimation",
      "topics": [
        "estimateCellCounts"
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    },
    {
      "page": "fixMethOutliers",
      "title": "Fix methylation outliers",
      "topics": [
        "fixMethOutliers"
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    },
    {
      "page": "gaphunter",
      "title": "Find gap signals in 450k data",
      "topics": [
        "gaphunter"
      ]
    },
    {
      "page": "GenomicMethylSet-class",
      "title": "GenomicMethylSet instances",
      "topics": [
        "annotation,GenomicMethylSet-method",
        "annotation<-,GenomicMethylSet,ANY-method",
        "combine,GenomicMethylSet,GenomicMethylSet-method",
        "featureNames,GenomicMethylSet-method",
        "featureNames<-,GenomicMethylSet-method",
        "GenomicMethylSet",
        "GenomicMethylSet-class",
        "getBeta,GenomicMethylSet-method",
        "getCN,GenomicMethylSet-method",
        "getM,GenomicMethylSet-method",
        "getMeth,GenomicMethylSet-method",
        "getUnmeth,GenomicMethylSet-method",
        "mapToGenome,GenomicMethylSet-method",
        "pData,GenomicMethylSet-method",
        "pData<-,GenomicMethylSet,DataFrame-method",
        "preprocessMethod,GenomicMethylSet-method",
        "sampleNames,GenomicMethylSet-method",
        "sampleNames<-,GenomicMethylSet,ANY-method",
        "show,GenomicMethylSet-method"
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    {
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      "title": "GenomicRatioSet instances",
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        "annotation<-,GenomicRatioSet,ANY-method",
        "combine,GenomicRatioSet,GenomicRatioSet-method",
        "featureNames,GenomicRatioSet-method",
        "featureNames<-,GenomicRatioSet-method",
        "GenomicRatioSet",
        "GenomicRatioSet-class",
        "getBeta,GenomicRatioSet-method",
        "getCN",
        "getCN,GenomicRatioSet-method",
        "getM,GenomicRatioSet-method",
        "mapToGenome,GenomicRatioSet-method",
        "pData,GenomicRatioSet-method",
        "pData<-,GenomicRatioSet,DataFrame-method",
        "preprocessMethod,GenomicRatioSet-method",
        "sampleNames,GenomicRatioSet-method",
        "sampleNames<-,GenomicRatioSet,ANY-method",
        "show,GenomicRatioSet-method"
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    },
    {
      "page": "getAnnotation",
      "title": "Accessing annotation for Illumina methylation objects",
      "topics": [
        "addSnpInfo",
        "dropLociWithSnps",
        "getAnnotation",
        "getAnnotationObject",
        "getIslandStatus",
        "getLocations",
        "getProbeType",
        "getSnpInfo"
      ]
    },
    {
      "page": "getGenomicRatioSetFromGEO",
      "title": "Reading Illumina methylation array data from GEO.",
      "topics": [
        "getGenomicRatioSetFromGEO"
      ]
    },
    {
      "page": "utils",
      "title": "Various utilities",
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      "page": "getQC",
      "title": "Estimate sample-specific quality control (QC) for methylation data",
      "topics": [
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      "page": "getSex",
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      "topics": [
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        "IlluminaMethylationAnnotation-class",
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      "page": "IlluminaMethylationManifest-class",
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      "topics": [
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        "getManifest",
        "getManifest,character-method",
        "getManifest,IlluminaMethylationManifest-method",
        "getManifestInfo",
        "getProbeInfo",
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        "IlluminaMethylationManifest-class",
        "show,IlluminaMethylationManifest-method"
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      "page": "logit2",
      "title": "logit in base 2.",
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        "logit2"
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      "page": "makeGenomicRatioSetFromMatrix",
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      "page": "mapToGenome-methods",
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        "mapToGenome,RatioSet-method",
        "mapToGenome,RGChannelSet-method",
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      "page": "mdsPlot",
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      "page": "MethylSet-class",
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      "page": "minfiQC",
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      "page": "plotCpg",
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      "page": "preprocessFunnorm",
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      "page": "preprocessIllumina",
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        "preprocessIllumina"
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      "page": "preprocessNoob",
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      "page": "preprocessQuantile",
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      "page": "preprocessRaw",
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      "page": "preprocessSwan",
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      "page": "ratioConvert-methods",
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      "page": "read.metharray",
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      "title": "The minfi User's Guide",
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        "Citing the minfi package",
        "Terminology",
        "Dependencies",
        "minfi classes",
        "Reading data",
        "Advanced notes on Reading Data",
        "Manifest / annotation",
        "What everyone needs to know",
        "Advanced discussion",
        "Quality control",
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        "SNPs and other issues",
        "Identifying differentially methylated regions",
        "Correcting for cell type heterogenity",
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