{
  "_id": "6ac8adc1de46216d5edd5840",
  "Package": "gcapc",
  "Title": "GC Aware Peak Caller",
  "Version": "1.36.0",
  "Author": "Mingxiang Teng and Rafael A. Irizarry",
  "Maintainer": "Mingxiang Teng <tengmx@gmail.com>",
  "Description": "Peak calling for ChIP-seq data with consideration of\npotential GC bias in sequencing reads. GC bias is first\nestimated with generalized linear mixture models using\neffective GC strategy, then applied into peak significance\nestimation.",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/tengmx/gcapc",
  "License": "GPL-3",
  "biocViews": "Sequencing, ChIPSeq, BatchEffect, PeakDetection",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:44:47 UTC",
  "RemoteUrl": "https://github.com/bioc/gcapc",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 08:51:37 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "gcapc_1.36.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/907744dced19aa30f5ad00f43f6c8860b40bd209bfa81be6370216be31f880e9",
  "_filesize": 3905917,
  "_sha256": "907744dced19aa30f5ad00f43f6c8860b40bd209bfa81be6370216be31f880e9",
  "_expires": "2027-01-17T09:02:55.000Z",
  "_created": "2026-10-09T08:51:37.000Z",
  "_published": "2026-10-09T09:02:57.701Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 11
  },
  "_upstream": "https://github.com/bioc/gcapc",
  "_commit": {
    "id": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380287
  },
  "_maintainer": {
    "name": "Mingxiang Teng",
    "email": "tengmx@gmail.com",
    "login": "tengmx",
    "description": "Bioinformatics",
    "uuid": 5973324
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113744916745,
      "time": 213,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11605795618"
    },
    {
      "job": 113744916909,
      "time": 615,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11605187966"
    },
    {
      "job": 113744916854,
      "time": 535,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11606195264"
    },
    {
      "job": 113744916862,
      "time": 350,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11605810631"
    },
    {
      "job": 113744916886,
      "time": 489,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11605227470"
    },
    {
      "job": 113742350685,
      "time": 446,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11604219646"
    },
    {
      "job": 113744917006,
      "time": 234,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11605845725"
    },
    {
      "job": 113744916910,
      "time": 338,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11605686524"
    },
    {
      "job": 113744916929,
      "time": 460,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11605526814"
    },
    {
      "job": 113744917078,
      "time": 381,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11605731473"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm10",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "sequencing",
    "chipseq",
    "batcheffect",
    "peakdetection"
  ],
  "_stars": 10,
  "_contributors": [
    {
      "user": "tengmx",
      "count": 61,
      "uuid": 5973324
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 474,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 618,
    "source": "https://www.bioconductor.org/packages/stats/bioc/gcapc"
  },
  "_devurl": "https://github.com/tengmx/gcapc",
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gcapc.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/tengmx/gcapc",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bindWidth",
    "gcapcPeaks",
    "gcEffects",
    "peaksCAT",
    "read5endCoverage",
    "refinePeaks",
    "refineSites"
  ],
  "_help": [
    {
      "page": "bindWidth",
      "title": "ChIP-seq Binding Width And Peak Window Size Estimation",
      "topics": [
        "bindWidth"
      ]
    },
    {
      "page": "gcapcPeaks",
      "title": "GC Effects Aware Peak Calling",
      "topics": [
        "gcapcPeaks"
      ]
    },
    {
      "page": "gcEffects",
      "title": "ChIP-seq GC Effects Estimation",
      "topics": [
        "gcEffects"
      ]
    },
    {
      "page": "peaksCAT",
      "title": "CATplot of Peaks",
      "topics": [
        "peaksCAT"
      ]
    },
    {
      "page": "read5endCoverage",
      "title": "Reads Coverage Using 5-end Base",
      "topics": [
        "read5endCoverage"
      ]
    },
    {
      "page": "refinePeaks",
      "title": "Refine Peaks with GC Effects",
      "topics": [
        "refinePeaks"
      ]
    },
    {
      "page": "refineSites",
      "title": "Adjust ChIP-seq Read Count Table",
      "topics": [
        "refineSites"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/gcapc/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "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": "gcapc.Rmd",
      "filename": "gcapc.html",
      "title": "The gcapc user's guide",
      "author": "| Mingxiang Teng mxteng@jimmy.harvard.edu | Rafael A. Irizarry rafa@jimmy.harvard.edu | Department of Biostatistics, Dana-Farber Cancer Institute & | Harvard T.H. Chan School of Public Health, Boston, MA, USA",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "Preparing Inputs",
        "Peak Calling/Refining",
        "Reads coverage",
        "Binding width",
        "GC effects",
        "Peak significance",
        "Peak refining",
        "Correcting GC Effects for A Count Table",
        "Summary",
        "References"
      ],
      "created": "2016-10-19 15:02:19",
      "modified": "2017-06-08 19:17:18",
      "commits": 19
    }
  ],
  "_score": 5,
  "_indexed": false,
  "_nocasepkg": "gcapc",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/gcapc",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.36.0",
      "date": "2026-10-09T08:58:10.000Z",
      "distro": "resolute",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/c650338360b948f29b0c04459913b92c8c1e2084d24f7695a3bca8dcf6448949",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.36.0",
      "date": "2026-10-09T08:57:46.000Z",
      "distro": "resolute",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/cde3fdb057d78b3be95c8645622f4b00b2d50e473cdf37742276d08eda20cbf9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.36.0",
      "date": "2026-10-09T08:54:25.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/78084f176bd8712c8102b7d8687e921d8e16c23564b88545251fdac67e354633",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.36.0",
      "date": "2026-10-09T08:55:42.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/f0386805bef481945f8c3b71cba9797dd4da2e32cd942eebbc86e0b9ea548055",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.36.0",
      "date": "2026-10-09T08:56:10.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/1a4186d1d88324d505cc92084c07e4863b4b65a5314149a123dfd9b7d5a8b1b1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-10-09T08:54:06.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/9b22009001aa59a4c14e6291acce92eca11ec7f5650a1aa923fdc3b961be690e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-10-09T08:54:49.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/c69fb243125f9b34a0046c7382a840dcf49de8aa30ed4611a9ee7e42925406f7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-10-09T08:54:56.000Z",
      "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0",
      "fileid": "https://r2.ropensci.org/010e3ee76946df5762927e40d39d6d1af2b996e17507e5c32f07b8423a543bd4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37906846062"
    }
  ]
}