{
  "_id": "6ae86e2e1e2c7b3a4f531e14",
  "Package": "BEAT",
  "Type": "Package",
  "Version": "1.51.0",
  "Title": "BEAT - BS-Seq Epimutation Analysis Toolkit",
  "Date": "2014-02-14",
  "Maintainer": "Kemal Akman <akman@mpipz.mpg.de>",
  "Author": "Kemal Akman <akman@mpipz.mpg.de>",
  "Description": "Model-based analysis of single-cell methylation data",
  "License": "LGPL (>= 3.0)",
  "Packaged": {
    "Date": "2026-11-02 10:55:06 UTC",
    "User": "root"
  },
  "biocViews": "ImmunoOncology, Genetics, MethylSeq, Software,\nDNAMethylation, Epigenetics",
  "Config/pak/sysreqs": "make libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:33 UTC",
  "RemoteUrl": "https://github.com/bioc/BEAT",
  "RemoteRef": "HEAD",
  "RemoteSha": "6c3988d029ea74187e52199fbf6130eb13938d5b",
  "NeedsCompilation": "no",
  "_user": "bioc",
  "_type": "src",
  "_file": "BEAT_1.51.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/4bffdbd4d8dbc3109af88d7aaaee30a81bfe3544234e0626a975292cd5f73f7d",
  "_filesize": 3493470,
  "_sha256": "4bffdbd4d8dbc3109af88d7aaaee30a81bfe3544234e0626a975292cd5f73f7d",
  "_expires": "2027-02-10T11:04:12.000Z",
  "_created": "2026-11-02T10:55:06.000Z",
  "_published": "2026-11-02T11:04:14.385Z",
  "_upstream": "https://github.com/bioc/BEAT",
  "_status": "success",
  "_maintainer": {
    "name": "Kemal Akman",
    "email": "akman@mpipz.mpg.de"
  },
  "_jobs": [
    {
      "job": 125234838168,
      "time": 142,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13134429629"
    },
    {
      "job": 125234838760,
      "time": 492,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13135432422"
    },
    {
      "job": 125234838030,
      "time": 311,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13134484861"
    },
    {
      "job": 125234838018,
      "time": 217,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13135676184"
    },
    {
      "job": 125234838136,
      "time": 258,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13136000403"
    },
    {
      "job": 125232813867,
      "time": 280,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13135530484"
    },
    {
      "job": 125234837966,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13135011398"
    },
    {
      "job": 125234838126,
      "time": 300,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13134867778"
    },
    {
      "job": 125234838124,
      "time": 286,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13135486260"
    },
    {
      "job": 125234838051,
      "time": 277,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13135421702"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597",
  "_commit": {
    "id": "6c3988d029ea74187e52199fbf6130eb13938d5b",
    "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": 1777379913
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.13.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ShortRead",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "genetics",
    "methylseq",
    "software",
    "dnamethylation",
    "epigenetics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 483,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 668,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BEAT"
  },
  "_mentions": 54,
  "_searchresults": 7,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/BEAT.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "epimutation_calls",
    "generate_results",
    "makeParams",
    "positions_to_regions"
  ],
  "_datasets": [
    {
      "name": "positions",
      "title": "Sample dataset of CpG positions for a single cell BS-seq sample",
      "object": "BEAT",
      "file": "BEAT.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "pos",
        "meth",
        "unmeth"
      ],
      "rows": 235935,
      "table": true,
      "tojson": true
    },
    {
      "name": "positions.reference",
      "title": "Sample dataset of CpG positions for a reference BS-Seq sample",
      "object": "BEAT",
      "file": "BEAT.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "pos",
        "meth",
        "unmeth"
      ],
      "rows": 237531,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "BEAT",
      "title": "BEAT - BS-Seq Epimutation Analysis Toolkit",
      "topics": [
        "BEAT-package",
        "BEAT"
      ]
    },
    {
      "page": "epimutation_calls",
      "title": "Returns epimutation rates and sites.",
      "topics": [
        "epimutation_calls"
      ]
    },
    {
      "page": "generate_results",
      "title": "Computes model methylation states for genomic region counts of a list of samples.",
      "topics": [
        "generate_results"
      ]
    },
    {
      "page": "makeParams",
      "title": "Creates a parameter object of arguments to be used with other BEAT functions.",
      "topics": [
        "makeParams"
      ]
    },
    {
      "page": "positions",
      "title": "Sample dataset of CpG positions for a single cell BS-seq sample",
      "topics": [
        "positions"
      ]
    },
    {
      "page": "positions_to_regions",
      "title": "Converts methylation counts for single genomic positions to counts for genomic regions",
      "topics": [
        "positions_to_regions"
      ]
    },
    {
      "page": "positions.reference",
      "title": "Sample dataset of CpG positions for a reference BS-Seq sample",
      "topics": [
        "positions.reference"
      ]
    }
  ],
  "_rundeps": [
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "deldir",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "hwriter",
    "interp",
    "IRanges",
    "jpeg",
    "jsonlite",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "MASS",
    "matrixStats",
    "mime",
    "openssl",
    "png",
    "pwalign",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Vectors",
    "Seqinfo",
    "ShortRead",
    "snow",
    "sys",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "BEAT.Rnw",
      "filename": "BEAT.pdf",
      "title": "Analysing single-cell BS-Seq data with the \"BEAT\" package",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-02-12 19:47:01",
      "modified": "2014-02-12 19:47:01",
      "commits": 1
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "beat",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-11-02T11:01:45.000Z",
      "distro": "resolute",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/c7f2b81cd205b76a13b9003acf9722f31a06803a923fd29a2c6c973d648dc26c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-11-02T10:59:07.000Z",
      "distro": "resolute",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/c04f547761f4bef29fdc371fb8c68f61e49057d174650e16051980afffdcfdbc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-11-02T10:57:15.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/0e7165014bd6ce6b1ba55778695a4dad5187b7c20489a8039e3b3cf1d54a59c2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-11-02T10:57:28.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/71664fc14cdf784b1ea05cc27083fcc5de06495ea15599cc496df6ea0c7e86ba",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.51.0",
      "date": "2026-11-02T10:57:49.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/a4e4d7f9859447acdfacbe92c8b4208e4a866aae2498f9c409dbcd5064c63ed6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-11-02T10:57:12.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/0fe79dafab98de562748d07e70c935f79c3758f4e7aec5aa57cc86b00ba94ce1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-11-02T10:56:56.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/2c3589f6b870a573d3e4059eade283ce7381280f0e497c9bb534d9bbf5dcca05",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-11-02T10:57:06.000Z",
      "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b",
      "fileid": "https://r2.ropensci.org/774c152d50c0312e002e1d0ec54f9200e8df6b7d262c57681e0bae4cdbd31b5e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41432009597"
    }
  ]
}