{
  "_id": "6a1af8ed1d7bb097a09fb2f6",
  "Package": "biscuiteer",
  "Type": "Package",
  "Title": "Convenience Functions for Biscuit",
  "Description": "A test harness for bsseq loading of Biscuit output,\nsummarization of WGBS data over defined regions and in mappable\nsamples, with or without imputation, dropping of mostly-NA\nrows, age estimates, etc.",
  "Version": "1.27.0",
  "Date": "2026-04-09",
  "Authors@R": "c(person(\"Tim\", \"Triche\", role = c(\"aut\")),\nperson(\"Wanding\", \"Zhou\", role = c(\"aut\")),\nperson(\"Benjamin\", \"Johnson\", role = c(\"aut\")),\nperson(\"Jacob\", \"Morrison\", role = c(\"aut\", \"cre\"),\nemail = \"jacob.morrison@vai.org\"),\nperson(\"Lyong\", \"Heo\", role = c(\"aut\")),\nperson(\"James\", \"Eapen\", role = c(\"aut\")))",
  "URL": "https://github.com/trichelab/biscuiteer",
  "BugReports": "https://github.com/trichelab/biscuiteer/issues",
  "License": "GPL-3",
  "biocViews": "DataImport, MethylSeq, DNAMethylation",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:16 UTC",
  "RemoteUrl": "https://github.com/bioc/biscuiteer",
  "RemoteRef": "HEAD",
  "RemoteSha": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:47:06 UTC",
    "User": "root"
  },
  "Author": "Tim Triche [aut],\nWanding Zhou [aut],\nBenjamin Johnson [aut],\nJacob Morrison [aut, cre],\nLyong Heo [aut],\nJames Eapen [aut]",
  "Maintainer": "Jacob Morrison <jacob.morrison@vai.org>",
  "MD5sum": "dd31e2c795cff773d778994cf7d1104a",
  "_user": "bioc",
  "_type": "src",
  "_file": "biscuiteer_1.27.0.tar.gz",
  "_fileid": "7f4dc80af8ffa53fac95a6fcd58592f0852a1f9c06458dde8ca76af61728f277",
  "_filesize": 4921348,
  "_sha256": "7f4dc80af8ffa53fac95a6fcd58592f0852a1f9c06458dde8ca76af61728f277",
  "_created": "2026-05-30T09:47:06.000Z",
  "_published": "2026-05-30T14:49:17.954Z",
  "_jobs": [
    {
      "job": 78640664382,
      "time": 484,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307525104"
    },
    {
      "job": 78640664385,
      "time": 730,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307547858"
    },
    {
      "job": 78640664389,
      "time": 867,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307561057"
    },
    {
      "job": 78640664386,
      "time": 469,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308993461"
    },
    {
      "job": 78640664390,
      "time": 525,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7309000229"
    },
    {
      "job": 78639719509,
      "time": 570,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307295490"
    },
    {
      "job": 78640664379,
      "time": 403,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307518526"
    },
    {
      "job": 78640664393,
      "time": 931,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307566012"
    },
    {
      "job": 78640664400,
      "time": 729,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307546254"
    },
    {
      "job": 78640664396,
      "time": 913,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307564434"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/biscuiteer",
  "_commit": {
    "id": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380676
  },
  "_maintainer": {
    "name": "Jacob Morrison",
    "email": "jacob.morrison@vai.org",
    "login": "jamorrison",
    "description": "Bioinformatics Research Scientist in the @huishenlab.",
    "uuid": 7786080
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "biscuiteerData",
      "role": "Depends"
    },
    {
      "package": "bsseq",
      "role": "Depends"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "qualV",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "HDF5Array",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "Mus.musculus",
      "role": "Imports"
    },
    {
      "package": "Homo.sapiens",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "QDNAseq",
      "role": "Imports"
    },
    {
      "package": "dmrseq",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rlang",
      "role": "Suggests"
    },
    {
      "package": "scmeth",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "QDNAseq.hg19",
      "role": "Suggests"
    },
    {
      "package": "QDNAseq.mm10",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dataimport",
    "methylseq",
    "dnamethylation"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "ttriche",
      "count": 166,
      "uuid": 4386
    },
    {
      "user": "jamorrison",
      "count": 49,
      "uuid": 7786080
    },
    {
      "user": "biobenkj",
      "count": 36,
      "uuid": 10948407
    },
    {
      "user": "jwokaty",
      "count": 18,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "jamespeapen",
      "count": 5,
      "uuid": 39574560
    },
    {
      "user": "heoly32",
      "count": 5,
      "uuid": 37587081
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "svad98",
      "count": 2,
      "uuid": 91341854
    },
    {
      "user": "kew24",
      "count": 2,
      "uuid": 56448994
    },
    {
      "user": "njspix",
      "count": 1,
      "uuid": 56930974
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 465,
    "source": "https://www.bioconductor.org/packages/stats/bioc/biscuiteer"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/trichelab/biscuiteer",
  "_searchresults": 17,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/biscuiteer.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/trichelab/biscuiteer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "atRegions",
    "binCoverage",
    "biscuitMetadata",
    "byChromArm",
    "byExtremality",
    "checkBiscuitBED",
    "condenseSampleNames",
    "extremality",
    "fexpit",
    "filterLoci",
    "fixAge",
    "fixed",
    "fixNAs",
    "flogit",
    "geno",
    "getClock",
    "getLogitFracMeth",
    "grToSeg",
    "header",
    "info",
    "makeBSseq",
    "meta",
    "readBiscuit",
    "readEpibed",
    "RRBSeq",
    "samples",
    "segToGr",
    "simplifySampleNames",
    "summarizeBsSeqOver",
    "tabixRetrieve",
    "unionize",
    "WGBSage",
    "WGBSeq"
  ],
  "_datasets": [
    {
      "name": "clocks",
      "title": "clocks",
      "object": "clocks",
      "file": "clocks.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "horvath",
        "horvathshrunk",
        "hannum",
        "skinandblood",
        "hg19chrom",
        "hg19start",
        "hg19end",
        "hg19HMMI",
        "hg19ENSR",
        "hg38chrom",
        "hg38start",
        "hg38end",
        "hg38HMMI",
        "hg38ENSR"
      ],
      "rows": 730,
      "table": true,
      "tojson": true
    },
    {
      "name": "ENSR_subset.hg19",
      "title": "ENSR_subset data from hg19 genome",
      "object": "ENSR_subset.hg19",
      "file": "ENSR_subset.hg19.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ENSR_subset.hg38",
      "title": "ENSR_subset data from hg38 genome",
      "object": "ENSR_subset.hg38",
      "file": "ENSR_subset.hg38.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GRCh37.chromArm",
      "title": "GRCh37.chromArm",
      "object": "GRCh37.chromArm",
      "file": "GRCh37.chromArm.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GRCh38.chromArm",
      "title": "GRCh38.chromArm",
      "object": "GRCh38.chromArm",
      "file": "GRCh38.chromArm.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "H9state23unmeth.hg19",
      "title": "H9state23unmeth.hg19",
      "object": "H9state23unmeth.hg19",
      "file": "H9state23unmeth.hg19.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "H9state23unmeth.hg38",
      "title": "H9state23unmeth.hg38",
      "object": "H9state23unmeth.hg38",
      "file": "H9state23unmeth.hg38.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hg19.chromArm",
      "title": "hg19.chromArm",
      "object": "hg19.chromArm",
      "file": "hg19.chromArm.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hg38.chromArm",
      "title": "hg38.chromArm",
      "object": "hg38.chromArm",
      "file": "hg38.chromArm.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HMM_CpG_islands.hg19",
      "title": "HMM_CpG_islands.hg19",
      "object": "HMM_CpG_islands.hg19",
      "file": "HMM_CpG_islands.hg19.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HMM_CpG_islands.hg38",
      "title": "HMM_CpG_islands.hg38",
      "object": "HMM_CpG_islands.hg38",
      "file": "HMM_CpG_islands.hg38.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seqinfo.hg19",
      "title": "seqinfo.hg19",
      "object": "seqinfo.hg19",
      "file": "seqinfo.hg19.rda",
      "class": [
        "Seqinfo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seqinfo.hg38",
      "title": "seqinfo.hg38",
      "object": "seqinfo.hg38",
      "file": "seqinfo.hg38.rda",
      "class": [
        "Seqinfo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "seqinfo.mm10",
      "title": "seqinfo.mm10",
      "object": "seqinfo.mm10",
      "file": "seqinfo.mm10.rda",
      "class": [
        "Seqinfo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "biscuiteer-package",
      "title": "Convenience Functions for Biscuit",
      "topics": [
        "biscuiteer-package",
        "biscuiteer",
        "_PACKAGE"
      ]
    },
    {
      "page": "atRegions",
      "title": "Summarize a bsseq dataset over defined regions",
      "topics": [
        "atRegions"
      ]
    },
    {
      "page": "binCoverage",
      "title": "Bin CpG or CpH coverage to simplify and improve CNA \"sketching\"",
      "topics": [
        "binCoverage"
      ]
    },
    {
      "page": "biscuiteer-methods",
      "title": "bsseq class methods (VCF-centric) added by biscuiteer",
      "topics": [
        "biscuiteer-methods",
        "BSseq-methods",
        "coverage",
        "fixed,BSseq-method",
        "geno,BSseq,ANY-method",
        "header",
        "header,BSseq-method",
        "info,BSseq-method",
        "meta,BSseq-method",
        "reference",
        "samples,BSseq-method"
      ]
    },
    {
      "page": "biscuitMetadata",
      "title": "Biscuit metadata from VCF header",
      "topics": [
        "biscuitMetadata",
        "getBiscuitMetadata"
      ]
    },
    {
      "page": "byChromArm",
      "title": "A simple parallization step",
      "topics": [
        "byChromArm"
      ]
    },
    {
      "page": "byExtremality",
      "title": "Choose loci or features by extremality",
      "topics": [
        "byExtremality"
      ]
    },
    {
      "page": "checkBiscuitBED",
      "title": "Inspect Biscuit VCF and BED files",
      "topics": [
        "checkBiscuitBED"
      ]
    },
    {
      "page": "clocks",
      "title": "clocks",
      "topics": [
        "clocks"
      ]
    },
    {
      "page": "condenseSampleNames",
      "title": "Simplify sample names for a bsseq object",
      "topics": [
        "condenseSampleNames"
      ]
    },
    {
      "page": "CpGindex",
      "title": "Measure methylation status for PRCs or PMDs",
      "topics": [
        "CpGindex"
      ]
    },
    {
      "page": "ENSR_subset.hg19",
      "title": "ENSR_subset data from hg19 genome",
      "topics": [
        "ENSR_subset.hg19"
      ]
    },
    {
      "page": "ENSR_subset.hg38",
      "title": "ENSR_subset data from hg38 genome",
      "topics": [
        "ENSR_subset.hg38"
      ]
    },
    {
      "page": "extremality",
      "title": "Compute fraction of a Bernoulli variance",
      "topics": [
        "extremality"
      ]
    },
    {
      "page": "fexpit",
      "title": "Helper function: expanded expit",
      "topics": [
        "fexpit"
      ]
    },
    {
      "page": "filterLoci",
      "title": "Filter loci with zero coverage",
      "topics": [
        "filterLoci"
      ]
    },
    {
      "page": "fixAge",
      "title": "Turn 'epigenetic clock' into actual age",
      "topics": [
        "fixAge"
      ]
    },
    {
      "page": "fixNAs",
      "title": "Replace NAs with another value",
      "topics": [
        "fixNAs"
      ]
    },
    {
      "page": "flogit",
      "title": "Helper function: squeezed logit",
      "topics": [
        "flogit"
      ]
    },
    {
      "page": "getClock",
      "title": "Retrieve 'epigenetic clock' models",
      "topics": [
        "getClock"
      ]
    },
    {
      "page": "getLogitFracMeth",
      "title": "Helper function for compartment inference",
      "topics": [
        "getLogitFracMeth",
        "getMvals"
      ]
    },
    {
      "page": "GRCh37.chromArm",
      "title": "GRCh37.chromArm",
      "topics": [
        "GRCh37.chromArm"
      ]
    },
    {
      "page": "GRCh38.chromArm",
      "title": "GRCh38.chromArm",
      "topics": [
        "GRCh38.chromArm"
      ]
    },
    {
      "page": "grToSeg",
      "title": "Dump GRanges to segmented data data.frame",
      "topics": [
        "grToSeg"
      ]
    },
    {
      "page": "H9state23unmeth.hg19",
      "title": "H9state23unmeth.hg19",
      "topics": [
        "H9state23unmeth.hg19"
      ]
    },
    {
      "page": "H9state23unmeth.hg38",
      "title": "H9state23unmeth.hg38",
      "topics": [
        "H9state23unmeth.hg38"
      ]
    },
    {
      "page": "hg19.chromArm",
      "title": "hg19.chromArm",
      "topics": [
        "hg19.chromArm"
      ]
    },
    {
      "page": "hg38.chromArm",
      "title": "hg38.chromArm",
      "topics": [
        "hg38.chromArm"
      ]
    },
    {
      "page": "HMM_CpG_islands.hg19",
      "title": "HMM_CpG_islands.hg19",
      "topics": [
        "HMM_CpG_islands.hg19"
      ]
    },
    {
      "page": "HMM_CpG_islands.hg38",
      "title": "HMM_CpG_islands.hg38",
      "topics": [
        "HMM_CpG_islands.hg38"
      ]
    },
    {
      "page": "makeBSseq",
      "title": "Make an in-memory bsseq object from a biscuit BED",
      "topics": [
        "makeBSseq"
      ]
    },
    {
      "page": "readBiscuit",
      "title": "Read biscuit output into bsseq object",
      "topics": [
        "loadBiscuit",
        "readBiscuit"
      ]
    },
    {
      "page": "readEpibed",
      "title": "Read in and decode the RLE representation of the epibed format out of biscuit epiread",
      "topics": [
        "readEpibed"
      ]
    },
    {
      "page": "RRBSeq",
      "title": "(e)RRBS settings for dmrseq",
      "topics": [
        "RRBSeq"
      ]
    },
    {
      "page": "segToGr",
      "title": "Import a segmentation file into GRanges object",
      "topics": [
        "segToGr"
      ]
    },
    {
      "page": "seqinfo.hg19",
      "title": "seqinfo.hg19",
      "topics": [
        "seqinfo.hg19"
      ]
    },
    {
      "page": "seqinfo.hg38",
      "title": "seqinfo.hg38",
      "topics": [
        "seqinfo.hg38"
      ]
    },
    {
      "page": "seqinfo.mm10",
      "title": "seqinfo.mm10",
      "topics": [
        "seqinfo.mm10"
      ]
    },
    {
      "page": "simplifySampleNames",
      "title": "Simplify bsseq sample names",
      "topics": [
        "simplifySampleNames"
      ]
    },
    {
      "page": "summarizeBsSeqOver",
      "title": "Summarize methylation over provided regions",
      "topics": [
        "summarizeBsSeqOver"
      ]
    },
    {
      "page": "tabixRetrieve",
      "title": "Read from tabix-indexed bed file to list objects",
      "topics": [
        "tabixRetrieve"
      ]
    },
    {
      "page": "unionize",
      "title": "Combine bsseq objects together without losing information",
      "topics": [
        "unionize"
      ]
    },
    {
      "page": "WGBSage",
      "title": "Guess ages using Horvath-style 'clock' models",
      "topics": [
        "WGBSage"
      ]
    },
    {
      "page": "WGBSeq",
      "title": "Wrapper for WGBS settings for dmrseq",
      "topics": [
        "WGBSeq"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/biscuiteer/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "annotatr",
    "askpass",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "biscuiteerData",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bsseq",
    "bumphunter",
    "cachem",
    "CGHbase",
    "CGHcall",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "dmrseq",
    "DNAcopy",
    "doRNG",
    "dplyr",
    "ExperimentHub",
    "farver",
    "fastmap",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "globals",
    "glue",
    "GO.db",
    "graph",
    "gtable",
    "gtools",
    "h5mread",
    "HDF5Array",
    "hms",
    "Homo.sapiens",
    "httr",
    "httr2",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "listenv",
    "locfit",
    "magrittr",
    "marray",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "Mus.musculus",
    "nlme",
    "openssl",
    "org.Hs.eg.db",
    "org.Mm.eg.db",
    "OrganismDbi",
    "outliers",
    "parallelly",
    "permute",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "QDNAseq",
    "qualV",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "regioneR",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "snowfall",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "TxDb.Mmusculus.UCSC.mm10.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "biscuiteer.Rmd",
      "filename": "biscuiteer.html",
      "title": "Biscuiteer User Guide",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Biscuiteer",
        "Quick Start",
        "Installing",
        "Loading Methylation Data",
        "Combining Methylation Results",
        "Loading epiBED files",
        "Analysis Functionality",
        "Inputs for A/B Compartment Inference",
        "Age Estimation"
      ],
      "created": "2019-10-17 14:33:05",
      "modified": "2023-12-06 17:12:19",
      "commits": 8
    }
  ],
  "_score": 6.184691430817599,
  "_indexed": true,
  "_nocasepkg": "biscuiteer",
  "_universes": [
    "bioc",
    "jamorrison",
    "trichelab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:28:27.000Z",
      "distro": "noble",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "0e4b9ecd10cf862d8f7e15a161b33d26aab9d57d6521db06f82e3a905cc8cb6b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:30:05.000Z",
      "distro": "noble",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "339afa3ce129fb9954cc7ae412ae60b6f2edf59b415acfae506468de1718147b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:42:59.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "2c01e17c28f68a1f51dd45df78440c73c9c8f2fe1bb3c965d333a7379955f32e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:43:12.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "7b1cd3aceb1eedbc25c26843bd8f86666b56875657476b04ae5a46f14ee4e684",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-05-30T10:29:00.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "3bf78993516af22e6491a7a22420f981a357aa16ecc50763fe29c80d2fb433d2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:29:10.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "bdcaad5116ea0e369c2680a248a054d665be03d7b31e17bcd6c2e60046b63099",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:27:50.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "743d88dd3154246ff1928c43eb2b339dfd39f936983d3dd522deab7d51557868",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:29:03.000Z",
      "commit": "54b494ab2f93541bd04c6b8b6a4a11004545e728",
      "fileid": "601eb3ad8699a9583288bc8eff7f874d0a4de1dba680c8d9605419250f2012b0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676383865"
    }
  ]
}