{
  "_id": "69d87daec5259ad4cd7fd746",
  "Package": "ChIPComp",
  "Type": "Package",
  "Title": "Quantitative comparison of multiple ChIP-seq datasets",
  "Version": "1.41.0",
  "Author": "Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang",
  "Maintainer": "Li Chen <li.chen@emory.edu>",
  "Description": "ChIPComp detects differentially bound sharp binding sites\nacross multiple conditions considering matching control.",
  "License": "GPL",
  "LazyLoad": "yes",
  "biocViews": "ChIPSeq, Sequencing, Transcription, Genetics,Coverage,\nMultipleComparison, DataImport",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2025-10-29 14:27:22 UTC",
  "RemoteUrl": "https://github.com/bioc/ChIPComp",
  "RemoteRef": "HEAD",
  "RemoteSha": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
  "Packaged": {
    "Date": "2026-04-08 09:20:28 UTC",
    "User": "root"
  },
  "MD5sum": "bcb6dafae943a82715fe6277682a8404",
  "_user": "bioc",
  "_type": "src",
  "_file": "ChIPComp_1.41.0.tar.gz",
  "_fileid": "8e2e2c37b29cff1da2045519c0c94612ea0609c68841f7a23fd520dd1a29e1b6",
  "_filesize": 713705,
  "_sha256": "8e2e2c37b29cff1da2045519c0c94612ea0609c68841f7a23fd520dd1a29e1b6",
  "_created": "2026-04-08T09:20:28.000Z",
  "_jobs": [
    {
      "job": 70728308097,
      "time": 309,
      "config": "bioc-checks",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "6364287539"
    },
    {
      "job": 70728308237,
      "time": 219,
      "config": "linux-devel-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 70728308227,
      "time": 321,
      "config": "linux-devel-x86_64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 70728308413,
      "time": 410,
      "config": "linux-release-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6324323756"
    },
    {
      "job": 70728308245,
      "time": 482,
      "config": "linux-release-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6324345080"
    },
    {
      "job": 70728308360,
      "time": 323,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6325975766"
    },
    {
      "job": 70728308395,
      "time": 549,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6325699687"
    },
    {
      "job": 70728308187,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 70728308198,
      "time": 277,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 70728307962,
      "time": 416,
      "config": "source",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6324201905"
    },
    {
      "job": 70728308220,
      "time": 251,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "OK",
      "artifact": "6324276300"
    },
    {
      "job": 70728308175,
      "time": 203,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 70728308406,
      "time": 335,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6324301443"
    },
    {
      "job": 70728308163,
      "time": 157,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/24127634696",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ChIPComp",
  "_commit": {
    "id": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
    "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_22 branch\n",
    "time": 1761748042
  },
  "_maintainer": {
    "name": "Li Chen",
    "email": "li.chen@emory.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "rtracklayer",
      "role": "Depends"
    },
    {
      "package": "Seqinfo",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm9",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-16",
      "n": 2
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.23"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.22"
    }
  ],
  "_topics": [
    "chipseq",
    "sequencing",
    "transcription",
    "genetics",
    "coverage",
    "multiplecomparison",
    "dataimport"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 444,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ChIPComp"
  },
  "_mentions": 3,
  "_searchresults": 52,
  "_rbuild": "4.5.3",
  "_assets": [
    "extra/ChIPComp.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ChIPComp",
    "makeConf",
    "makeCountSet"
  ],
  "_datasets": [
    {
      "name": "seqData",
      "title": "A 'ChIPComp' object.",
      "object": "seqData",
      "file": "seqData.rda",
      "class": [
        "ChIPComp"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ChIPComp-package",
      "title": "Detect differential binding sites for ChIP sequencing data",
      "topics": [
        "ChIPComp-package"
      ]
    },
    {
      "page": "ChIPComp",
      "title": "Perform hypothesis testing to detect differential binding sites",
      "topics": [
        "ChIPComp"
      ]
    },
    {
      "page": "makeConf",
      "title": "make configurations for experimental design written in csv sheet",
      "topics": [
        "makeConf"
      ]
    },
    {
      "page": "makeCountSet",
      "title": "make differential binding sites data frame",
      "topics": [
        "makeCountSet"
      ]
    },
    {
      "page": "plot",
      "title": "plot correlation between log ChIP read counts and smoothing control counts in common binding sites.",
      "topics": [
        "plot.ChIPComp"
      ]
    },
    {
      "page": "print",
      "title": "Print top ranked differential binding sites",
      "topics": [
        "print.ChIPComp"
      ]
    },
    {
      "page": "seqData",
      "title": "A 'ChIPComp' object.",
      "topics": [
        "seqData"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "BSgenome.Hsapiens.UCSC.hg19",
    "BSgenome.Mmusculus.UCSC.mm9",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "limma",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "sys",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "ChIPComp.Rnw",
      "filename": "ChIPComp.pdf",
      "title": "ChIPComp",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2015-08-13 21:21:16",
      "modified": "2020-04-25 20:03:39",
      "commits": 6
    }
  ],
  "_score": 4.670245853074125,
  "_indexed": true,
  "_nocasepkg": "chipcomp",
  "_universes": [
    "bioc"
  ],
  "_failure": {
    "version": "1.43.0",
    "commit": {
      "id": "e0f191c596f5aab879dcbfa74d993ace17790fec",
      "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": 1777380103
    },
    "buildurl": "https://github.com/r-universe/bioc/actions/runs/26847458965",
    "date": "2026-06-05T06:04:43.455Z",
    "job": {
      "job": 79672734721,
      "time": 299,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7429909014"
    }
  },
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-04-08T11:05:16.000Z",
      "arch": "aarch64",
      "commit": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
      "fileid": "e3556e901576afccb4c1fe5d9a4bc64bcb60c308023353569f30e7d1243930cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24127634696"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-04-08T10:45:18.000Z",
      "arch": "x86_64",
      "commit": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
      "fileid": "a45af98ae3786aef4e905b3d47c6e260cddafc109a049ce18279ca2e0bd8774e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24127634696"
    },
    {
      "r": "4.5.1",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-04-08T09:25:22.000Z",
      "arch": "emscripten",
      "commit": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
      "fileid": "f1f19fc610ace5e5f012563d9f348f532e86d90865bf4281d2f47fed9da2fd23",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24127634696"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-04-08T09:23:49.000Z",
      "arch": "x86_64",
      "commit": "6f90f756b7578d2b97a9af63309c53a4b1a881ad",
      "fileid": "2a9f966c5753c047fa138ca7cf51c077bd6fc2088d849baa281ad6a09ccef2a7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/24127634696"
    }
  ]
}