{
  "_id": "6aae3ce83d719c1f84079e1b",
  "Package": "GreyListChIP",
  "Type": "Package",
  "Version": "1.45.0",
  "Title": "Grey Lists -- Mask Artefact Regions Based on ChIP Inputs",
  "Date": "2025-07-22",
  "Authors@R": "c(person(\"Matt\",\"Eldridge\", email=\"matthew.eldridge@cruk.cam.ac.uk\",\nrole = c(\"cre\")),\nperson(\"Gord\",\"Brown\",email=\"DECEASED\",\nrole=\"aut\"))",
  "Description": "Identify regions of ChIP experiments with high signal in\nthe input, that lead to spurious peaks during peak calling.\nRemove reads aligning to these regions prior to peak calling,\nfor cleaner ChIP analysis.",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "biocViews": "ChIPSeq, Alignment, Preprocessing, DifferentialPeakCalling,\nSequencing, GenomeAnnotation, Coverage",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:30 UTC",
  "RemoteUrl": "https://github.com/bioc/GreyListChIP",
  "RemoteRef": "HEAD",
  "RemoteSha": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-19 07:21:06 UTC",
    "User": "root"
  },
  "Author": "Matt Eldridge [cre],\nGord Brown [aut]",
  "Maintainer": "Matt Eldridge <matthew.eldridge@cruk.cam.ac.uk>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GreyListChIP_1.45.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/f2682f3604811a7d4ac3cc540cf40ca71ee8f656c154ab4b580a4db59b82e148",
  "_filesize": 479493,
  "_sha256": "f2682f3604811a7d4ac3cc540cf40ca71ee8f656c154ab4b580a4db59b82e148",
  "_expires": "2026-12-28T07:42:30.000Z",
  "_created": "2026-09-19T07:21:06.000Z",
  "_published": "2026-09-19T07:42:32.267Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952",
  "_status": "success",
  "_upstream": "https://github.com/bioc/GreyListChIP",
  "_commit": {
    "id": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
    "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": 1777380030
  },
  "_maintainer": {
    "name": "Matt Eldridge",
    "email": "matthew.eldridge@cruk.cam.ac.uk",
    "login": "eldrid01",
    "description": "",
    "uuid": 5559069
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105860347720,
      "time": 238,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10579962065"
    },
    {
      "job": 105860347700,
      "time": 493,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10580490519"
    },
    {
      "job": 105860347738,
      "time": 529,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10580825110"
    },
    {
      "job": 105860347758,
      "time": 330,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10580746028"
    },
    {
      "job": 105860347712,
      "time": 377,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10579829968"
    },
    {
      "job": 105859650276,
      "time": 316,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10579499786"
    },
    {
      "job": 105860347718,
      "time": 206,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10580650008"
    },
    {
      "job": 105860347723,
      "time": 282,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10580500171"
    },
    {
      "job": 105860347745,
      "time": 301,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10580520269"
    },
    {
      "job": 105860347867,
      "time": 326,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10579724867"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 4,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.45.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.44.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "chipseq",
    "alignment",
    "preprocessing",
    "differentialpeakcalling",
    "sequencing",
    "genomeannotation",
    "coverage"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 468,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2069,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GreyListChIP"
  },
  "_mentions": 2,
  "_searchresults": 19,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GreyListChIP.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calcThreshold",
    "countReads",
    "export",
    "getKaryotype",
    "greyListBS",
    "loadKaryotype",
    "makeGreyList",
    "setRegions",
    "show"
  ],
  "_datasets": [
    {
      "name": "ce10.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "ce10.blacklist",
      "file": "ce10.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce11.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "ce11.blacklist",
      "file": "ce11.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dm3.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "dm3.blacklist",
      "file": "dm3.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dm6.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "dm6.blacklist",
      "file": "dm6.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "grch37.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "grch37.blacklist",
      "file": "grch37.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "grch38.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "grch38.blacklist",
      "file": "grch38.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "greyList",
      "title": "A sample 'GreyList' object for use in examples.",
      "object": "greyList",
      "file": "greyList.RData",
      "class": [
        "GreyList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hg19.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "hg19.blacklist",
      "file": "hg19.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hg38.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "hg38.blacklist",
      "file": "hg38.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mm10.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "mm10.blacklist",
      "file": "mm10.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mm9.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "object": "mm9.blacklist",
      "file": "mm9.blacklist.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "calcThreshold-methods",
      "title": "Calculate Read Count Threshold",
      "topics": [
        "calcThreshold",
        "calcThreshold,GreyList-method"
      ]
    },
    {
      "page": "ce10.blacklist",
      "title": "A 'GRanges' object representing ENCODE signal artefact or \"black list\" regions.",
      "topics": [
        "ce10.blacklist",
        "ce11.blacklist",
        "dm3.blacklist",
        "dm6.blacklist",
        "grch37.blacklist",
        "grch38.blacklist",
        "hg19.blacklist",
        "hg38.blacklist",
        "mm10.blacklist",
        "mm9.blacklist"
      ]
    },
    {
      "page": "countReads-methods",
      "title": "Count reads from a 'BamFile'",
      "topics": [
        "countReads",
        "countReads,GreyList-method"
      ]
    },
    {
      "page": "getKaryotype-methods",
      "title": "Replace the karyotype of a 'GreyList' object",
      "topics": [
        "getKaryotype",
        "getKaryotype,GreyList-method"
      ]
    },
    {
      "page": "greyList",
      "title": "A sample 'GreyList' object for use in examples.",
      "topics": [
        "greyList"
      ]
    },
    {
      "page": "GreyList-class",
      "title": "'\"GreyList\"' Objects",
      "topics": [
        "export,GreyList,character,missing-method",
        "GreyList",
        "GreyList-class",
        "initialize,GreyList,BSgenome-method",
        "show,GreyList-method"
      ]
    },
    {
      "page": "greyListBS",
      "title": "Construct a grey list with default arguments",
      "topics": [
        "greyListBS"
      ]
    },
    {
      "page": "loadKaryotype-methods",
      "title": "Load a karyotype from a file",
      "topics": [
        "loadKaryotype",
        "loadKaryotype,GreyList-method"
      ]
    },
    {
      "page": "makeGreyList-methods",
      "title": "Generate a grey list from a 'GreyList' object",
      "topics": [
        "makeGreyList",
        "makeGreyList,GreyList-method"
      ]
    },
    {
      "page": "setRegions-methods",
      "title": "Replace the set of regions of a 'GreyList' object",
      "topics": [
        "setRegions",
        "setRegions,GreyList-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "GreyList-demo.Rnw",
      "filename": "GreyList-demo.pdf",
      "title": "Generating Grey Lists from Input Libraries",
      "engine": "utils::Sweave",
      "headings": [
        "1 Introduction",
        "2 Generating a Grey List",
        "3 Sample Data",
        "4 Obtaining Karyotypes",
        "5 Acknowledgements",
        "6 Session Info"
      ],
      "created": "2015-01-14 23:51:05",
      "modified": "2020-07-29 14:32:28",
      "commits": 3
    }
  ],
  "_score": 5.275755328994151,
  "_indexed": true,
  "_nocasepkg": "greylistchip",
  "_universes": [
    "bioc",
    "eldrid01"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-09-19T07:26:22.000Z",
      "distro": "resolute",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/7157f15314f4dd7dad844d3c857da52042d36198b8912dcf5cbcc549b5731799",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-09-19T07:28:16.000Z",
      "distro": "resolute",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/854fb2140a728076e029da345010f874000dac111ab99e391b06013b18ef3cdd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-09-19T07:38:51.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/1eb7aeda177666dc845fe1836029dceef252e4f205e72e684635edb83ea22a74",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-09-19T07:31:33.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/454a5747da7e433d74a1d9d9efa7d1cc12c33d99c4ad4a4c5827af5082bdd57c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.0",
      "date": "2026-09-19T07:25:06.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/6315c072db500fbcdcd01877411422601da3b8ad9cd77d9b17a668f8bfcda6cd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-09-19T07:23:34.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/0ad14ce0b6d2ec4b0bec545816e4dec94cc70eaeea2c1425ed3544b0d431f7f4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-09-19T07:23:39.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/c760e4c6e44a8a42ec20e8657ebd6adc24d8adf5a9556aba63558dc0e6c39ec2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-09-19T07:24:01.000Z",
      "commit": "47016f195078dfe25b4a9209050cd969a6bf9e8a",
      "fileid": "https://r2.ropensci.org/a20954050607c425494555f8406027cf1e8cb4cf246a311ac7b8b0c1c6c7b9a9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35428857952"
    }
  ]
}