{
  "_id": "6a197d04acfb0bcc41df6c39",
  "Package": "bsseq",
  "Version": "1.48.0",
  "Encoding": "UTF-8",
  "Title": "Analyze, manage and store whole-genome methylation data",
  "Description": "A collection of tools for analyzing and visualizing\nwhole-genome methylation data from sequencing. This includes\nwhole-genome bisulfite sequencing and Oxford nanopore data.",
  "Authors@R": "c(person(c(\"Kasper\", \"Daniel\"), \"Hansen\", role = c(\"aut\", \"cre\"),\nemail = \"kasperdanielhansen@gmail.com\", comment = c(ORCID = \"0000-0003-0086-0687\")),\nperson(\"Peter\", \"Hickey\", role = \"aut\", email = \"peter.hickey@gmail.com\", comment = c(ORCID = \"0000-0002-8153-6258\")),\nperson(\"Hervé\", \"Pagès\", role = \"ctb\"),\nperson(\"Aaron\", \"Lun\", role = \"ctb\"))",
  "Collate": "utils.R hasGRanges.R BSseq-class.R BSseqTstat_class.R\nBSseq_utils.R combine.R read.bismark.R read.bedMethyl.R\nread.modbam2bed.R read.modkit.R BSmooth.R BSmooth.tstat.R\ndmrFinder.R gof_stats.R plotting.R fisher.R permutations.R\nBSmooth.fstat.R BSseqStat_class.R getStats.R hdf5_utils.R\nDelayedArray_utils.R collapseBSseq.R FWIRanges-class.R\nFWGRanges-class.R findLoci.R Likelihood_functions.R",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/kasperdanielhansen/bsseq",
  "BugReports": "https://github.com/kasperdanielhansen/bsseq/issues",
  "biocViews": "DNAMethylation",
  "SystemRequirements": "C++17",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:41 UTC",
  "RemoteUrl": "https://github.com/bioc/bsseq",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a950720eb04ed59290104b8fa7448cc79fef190e",
  "Packaged": {
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    "User": "root"
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  "Author": "Kasper Daniel Hansen [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0086-0687>),\nPeter Hickey [aut] (ORCID: <https://orcid.org/0000-0002-8153-6258>),\nHervé Pagès [ctb],\nAaron Lun [ctb]",
  "Maintainer": "Kasper Daniel Hansen <kasperdanielhansen@gmail.com>",
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  "_exports": [
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    "assays",
    "binomialGoodnessOfFit",
    "BSmooth",
    "BSmooth.tstat",
    "BSseq",
    "BSseqStat",
    "BSseqTstat",
    "chrSelectBSseq",
    "collapseBSseq",
    "combine",
    "combineList",
    "data.frame2GRanges",
    "dmrFinder",
    "end",
    "end<-",
    "estimateErrorRate",
    "findLoci",
    "findOverlaps",
    "fisherTests",
    "getBSseq",
    "getCoverage",
    "getCpGMatrix",
    "getCpGs",
    "getMaxLikelihoodMatrix",
    "getMeth",
    "getStats",
    "granges",
    "hasBeenSmoothed",
    "ncol",
    "nrow",
    "orderBSseq",
    "overlapsAny",
    "pData",
    "pData<-",
    "plotManyRegions",
    "plotRegion",
    "poissonGoodnessOfFit",
    "read.bedMethyl",
    "read.bismark",
    "read.modbam2bed",
    "read.modkit",
    "sampleNames",
    "sampleNames<-",
    "seqlengths",
    "seqlengths<-",
    "seqlevels",
    "seqlevels<-",
    "seqnames",
    "seqnames<-",
    "show",
    "start",
    "start<-",
    "strand",
    "strand<-",
    "strandCollapse",
    "subsetByOverlaps",
    "updateObject",
    "width",
    "width<-"
  ],
  "_datasets": [
    {
      "name": "BS.chr22",
      "title": "Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.",
      "object": "BS.chr22",
      "file": "BS.chr22.rda",
      "class": [
        "BSseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "BS.chr22",
      "title": "Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.",
      "topics": [
        "BS.chr22"
      ]
    },
    {
      "page": "BSmooth",
      "title": "BSmooth, smoothing bisulfite sequence data",
      "topics": [
        "BSmooth"
      ]
    },
    {
      "page": "BSmooth.tstat",
      "title": "Compute t-statistics based on smoothed whole-genome bisulfite sequencing data.",
      "topics": [
        "BSmooth.tstat"
      ]
    },
    {
      "page": "BSseq",
      "title": "The constructor function for BSseq objects.",
      "topics": [
        "BSseq"
      ]
    },
    {
      "page": "BSseq-class",
      "title": "Class BSseq",
      "topics": [
        "assayNames,BSseq-method",
        "assays,BSseq-method",
        "BSseq-class",
        "chrSelectBSseq",
        "collapseBSseq",
        "combine,BSseq,BSseq-method",
        "combineList",
        "getBSseq",
        "hasBeenSmoothed",
        "length,BSseq-method",
        "orderBSseq",
        "pData,BSseq-method",
        "pData<-,BSseq,data.frame-method",
        "pData<-,BSseq,DataFrame-method",
        "sampleNames,BSseq-method",
        "sampleNames<-,BSseq,ANY-method",
        "show,BSseq-method",
        "strandCollapse",
        "updateObject,BSseq-method",
        "[,BSseq-method"
      ]
    },
    {
      "page": "bsseq-deprecated",
      "title": "Deprecated functions in package 'bsseq'",
      "topics": [
        "bsseq-deprecated"
      ]
    },
    {
      "page": "BSseqStat-class",
      "title": "Class BSseqStat",
      "topics": [
        "BSseqStat",
        "BSseqStat-class",
        "show,BSseqStat-method",
        "updateObject,BSseqStat-method",
        "[,BSseqStat,ANY,ANY,ANY-method",
        "[,BSseqStat-method"
      ]
    },
    {
      "page": "BSseqTstat-class",
      "title": "Class BSseqTstat",
      "topics": [
        "BSseqTstat",
        "BSseqTstat-class",
        "show,BSseqTstat-method",
        "updateObject,BSseqTstat-method",
        "[,BSseqTstat,ANY,ANY,ANY-method",
        "[,BSseqTstat-method"
      ]
    },
    {
      "page": "data.frame2GRanges",
      "title": "Converts a data frame to a GRanges.",
      "topics": [
        "data.frame2GRanges"
      ]
    },
    {
      "page": "dmrFinder",
      "title": "Finds differentially methylated regions for whole genome bisulfite sequencing data.",
      "topics": [
        "dmrFinder"
      ]
    },
    {
      "page": "estimateErrorRate",
      "title": "Estimate CpG-specific error rate from BSseq object.",
      "topics": [
        "estimateErrorRate"
      ]
    },
    {
      "page": "findLoci",
      "title": "Find methylation loci in a genome",
      "topics": [
        "findLoci"
      ]
    },
    {
      "page": "fisherTests",
      "title": "Compute Fisher-tests for a BSseq object",
      "topics": [
        "fisherTests"
      ]
    },
    {
      "page": "FWGRanges-class",
      "title": "Classes FWIRanges and FWGRanges",
      "topics": [
        "dimnames,arrayRealizationSink-method",
        "end,FWGRanges-method",
        "end,FWIRanges-method",
        "end<-,FWIRanges-method",
        "findOverlaps,FWGRanges,FWGRanges-method",
        "FWGRanges-class",
        "FWIRanges-class",
        "names,FWIRanges-method",
        "names<-,FWIRanges-method",
        "seqnames,FWGRanges-method",
        "start,FWGRanges-method",
        "start,FWIRanges-method",
        "start<-,FWIRanges-method",
        "strand,FWGRanges-method",
        "width,FWGRanges-method",
        "width,FWIRanges-method",
        "width<-,FWIRanges-method"
      ]
    },
    {
      "page": "getCoverage",
      "title": "Obtain coverage for BSseq objects.",
      "topics": [
        "getCoverage"
      ]
    },
    {
      "page": "getCpGMatrix",
      "title": "Generate a matrix of the most likely CpG status for a multi-sample BSseq object.",
      "topics": [
        "getCpGMatrix"
      ]
    },
    {
      "page": "getCpGs",
      "title": "Get CpG (and non-CpG) loci from a single sample BSseq object.",
      "topics": [
        "getCpGs"
      ]
    },
    {
      "page": "getMaxLikelihoodMatrix",
      "title": "Generate a matrix of the scaled likelihood of most likely CpG status for a multi-sample BSseq object.",
      "topics": [
        "getMaxLikelihoodMatrix"
      ]
    },
    {
      "page": "getMeth",
      "title": "Obtain methylation estimates for BSseq objects.",
      "topics": [
        "getMeth"
      ]
    },
    {
      "page": "getStats",
      "title": "Obtain statistics from a BSseqTstat object",
      "topics": [
        "getStats"
      ]
    },
    {
      "page": "goodnessOfFit",
      "title": "Binomial and poisson goodness of fit statistics for BSSeq objects",
      "topics": [
        "binomialGoodnessOfFit",
        "chisqGoodnessOfFit",
        "plot.chisqGoodnessOfFit",
        "poissonGoodnessOfFit",
        "print.chisqGoodnessOfFit"
      ]
    },
    {
      "page": "hasGRanges-class",
      "title": "Class hasGRanges",
      "topics": [
        "class:hasGRanges",
        "end,hasGRanges-method",
        "end<-,hasGRanges-method",
        "findOverlaps,GenomicRanges,hasGRanges-method",
        "findOverlaps,hasGRanges,GenomicRanges-method",
        "findOverlaps,hasGRanges,hasGRanges-method",
        "granges,hasGRanges-method",
        "hasGRanges",
        "hasGRanges-class",
        "length,hasGRanges-method",
        "overlapsAny,GenomicRanges,hasGRanges-method",
        "overlapsAny,hasGRanges,GenomicRanges-method",
        "overlapsAny,hasGRanges,hasGRanges-method",
        "seqlengths,hasGRanges-method",
        "seqlengths<-,hasGRanges-method",
        "seqlevels,hasGRanges-method",
        "seqlevels<-,hasGRanges-method",
        "seqnames,hasGRanges-method",
        "seqnames<-,hasGRanges-method",
        "start,hasGRanges-method",
        "start<-,hasGRanges-method",
        "strand,hasGRanges-method",
        "strand<-,hasGRanges,ANY-method",
        "strand<-,hasGRanges-method",
        "subsetByOverlaps,GenomicRanges,hasGRanges-method",
        "subsetByOverlaps,hasGRanges,GenomicRanges-method",
        "subsetByOverlaps,hasGRanges,hasGRanges-method",
        "width,hasGRanges-method",
        "width<-,hasGRanges-method",
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