{
  "_id": "6a1968d7acfb0bcc41de8a54",
  "Package": "ChIPexoQual",
  "Type": "Package",
  "Title": "ChIPexoQual",
  "Version": "1.36.0",
  "Author": "Rene Welch, Dongjun Chung, Sunduz Keles",
  "Maintainer": "Rene Welch <welch@stat.wisc.edu>",
  "Authors@R": "c(person(given = \"Dongjun\", family = \"Chung\", role = \"aut\"),\nperson(given = \"Sunduz\",family = \"Keles\",role = \"aut\"),\nperson(given = \"Rene\", family = \"Welch\", role = c(\"aut\",\n\"cre\"), email = \"[welch@stat.wisc.edu]\"))",
  "Description": "Package with a quality control pipeline for ChIP-exo/nexus\ndata.",
  "URL": "https:github.com/keleslab/ChIPexoQual",
  "BugReports": "https://github.com/welch16/ChIPexoQual/issues",
  "License": "GPL (>=2)",
  "VignetteBuilder": "knitr",
  "biocViews": "ChIPSeq, Sequencing, Transcription, Visualization,\nQualityControl, Coverage, Alignment",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:59 UTC",
  "RemoteUrl": "https://github.com/bioc/ChIPexoQual",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:15:16 UTC",
    "User": "root"
  },
  "MD5sum": "3fd335349a0af20b0fe7d4586cdbb7dc",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "ChIPexoQual_1.36.0.tar.gz",
  "_fileid": "52ffc41258f945180a5b6f0db780a7e5f83b97b80138d740c45ce5c899afe312",
  "_filesize": 2394122,
  "_sha256": "52ffc41258f945180a5b6f0db780a7e5f83b97b80138d740c45ce5c899afe312",
  "_created": "2026-05-29T08:15:16.000Z",
  "_published": "2026-05-29T10:22:15.214Z",
  "_jobs": [
    {
      "job": 78463801542,
      "time": 205,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7286264685"
    },
    {
      "job": 78463801600,
      "time": 500,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286354326"
    },
    {
      "job": 78463801534,
      "time": 515,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286359067"
    },
    {
      "job": 78463801570,
      "time": 276,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288417831"
    },
    {
      "job": 78463801531,
      "time": 422,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288459315"
    },
    {
      "job": 78462939317,
      "time": 364,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286204364"
    },
    {
      "job": 78463801566,
      "time": 179,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286257517"
    },
    {
      "job": 78463801610,
      "time": 519,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7286361183"
    },
    {
      "job": 78463801565,
      "time": 536,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7286366257"
    },
    {
      "job": 78463801585,
      "time": 549,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286370154"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ChIPexoQual",
  "_commit": {
    "id": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
    "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": 1777380299
  },
  "_maintainer": {
    "name": "Rene Welch",
    "email": "welch@stat.wisc.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "GenomicAlignments",
      "version": ">= 1.45.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.9.6",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "version": ">= 2.25.1",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 1.6",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.8",
      "role": "Imports"
    },
    {
      "package": "biovizBase",
      "version": ">= 1.18",
      "role": "Imports"
    },
    {
      "package": "broom",
      "version": ">= 0.4",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "version": ">= 1.1",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 0.5",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 0.4.0",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "version": ">= 0.3",
      "role": "Imports"
    },
    {
      "package": "hexbin",
      "version": ">= 1.27",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "ChIPexoQualExample",
      "version": ">= 0.99.1",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.10",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "version": ">= 2.2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "chipseq",
    "sequencing",
    "transcription",
    "visualization",
    "qualitycontrol",
    "coverage",
    "alignment"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "welch16",
      "count": 76,
      "uuid": 4492322
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "keles",
      "count": 2,
      "uuid": 5864569
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 510,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ChIPexoQual"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/welch16/chipexoqual",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/ChIPexoQual.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/welch16/chipexoqual",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ARCvURCplot",
    "beta1",
    "beta2",
    "calculateParamDist",
    "ExoData",
    "ExoDataBlacklist",
    "ExoDataSubsampling",
    "formatRegions",
    "FSRDistplot",
    "MAplot",
    "nreads",
    "paramDist",
    "paramDistBoxplot",
    "regionCompplot"
  ],
  "_datasets": [
    {
      "name": "blacklists",
      "title": "'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.",
      "object": "blacklists",
      "file": "blacklists.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exoExample",
      "title": "'ExoData' results for FoxA1 ChIP-exo experiment",
      "object": "exoExample",
      "file": "exoExample.RData",
      "class": [
        "ExoData"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ARCvURCplot",
      "title": "ARCvURCplot",
      "topics": [
        "ARCvURCplot"
      ]
    },
    {
      "page": "beta1-methods",
      "title": "beta1 methods",
      "topics": [
        "beta1",
        "beta1,ExoData-method"
      ]
    },
    {
      "page": "beta2-methods",
      "title": "beta2 methods",
      "topics": [
        "beta2",
        "beta2,ExoData-method"
      ]
    },
    {
      "page": "blacklists",
      "title": "'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.",
      "topics": [
        "blacklists"
      ]
    },
    {
      "page": "calculateParamDist",
      "title": "calculateParamDist 'calculateParamDist' calculates the quality parameters of one iteration. This function samples 'nregions' rows from the stat matrix and fits the linear model 'lm(d ~ 0 + u + w)'",
      "topics": [
        "calculateParamDist"
      ]
    },
    {
      "page": "ExoData",
      "title": "ExoData object and constructors",
      "topics": [
        "ExoData",
        "ExoData-class"
      ]
    },
    {
      "page": "ExoDataBlacklist",
      "title": "ExoDataBlacklist",
      "topics": [
        "ExoDataBlacklist"
      ]
    },
    {
      "page": "ExoDataSubsampling",
      "title": "ExoDataSubsampling",
      "topics": [
        "ExoDataSubsampling"
      ]
    },
    {
      "page": "exoExample",
      "title": "'ExoData' results for FoxA1 ChIP-exo experiment",
      "topics": [
        "exoExample"
      ]
    },
    {
      "page": "formatRegions",
      "title": "formatRegions 'formatRegions' separates the width, depth and uniquePos summary statistics from the 'ExoData' object to calculate the quality parameters/",
      "topics": [
        "formatRegions"
      ]
    },
    {
      "page": "FSRDistplot",
      "title": "FSRDistplot",
      "topics": [
        "FSRDistplot"
      ]
    },
    {
      "page": "MAplot",
      "title": "MAplot",
      "topics": [
        "MAplot"
      ]
    },
    {
      "page": "nreads-methods",
      "title": "nreads methods",
      "topics": [
        "nreads",
        "nreads,ExoData-method"
      ]
    },
    {
      "page": "paramDist-methods",
      "title": "paramDist methods",
      "topics": [
        "paramDist",
        "paramDist,ExoData-method"
      ]
    },
    {
      "page": "paramDistBoxplot",
      "title": "paramDistBoxplot",
      "topics": [
        "paramDistBoxplot"
      ]
    },
    {
      "page": "regionCompplot",
      "title": "regionCompplot",
      "topics": [
        "regionCompplot"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ChIPexoQual/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "broom",
    "BSgenome",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "dichromat",
    "digest",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "hexbin",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnet",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "ChIPexoQual: A quality control pipeline for ChIP-exo/nexus data.",
      "author": "| Rene Welch and Sündüz Keleş | Department of Statistics, University of Wisconsin-Madison",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Creating an ExoData object",
        "Enrichment analysis and library complexity:",
        "Strand imbalance",
        "Further exploration of ChIP-exo data",
        "Quality evaluation",
        "Subsampling reads from the experiment to asses quality",
        "Conclusions",
        "SessionInfo",
        "References"
      ],
      "created": "2016-07-18 21:11:40",
      "modified": "2018-01-24 23:44:49",
      "commits": 16
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": false,
  "_nocasepkg": "chipexoqual",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/ChIPexoQual",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.36.0",
      "date": "2026-05-29T08:19:09.000Z",
      "distro": "noble",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "0364e1e5cdbc04ce1b0084ca6d29fb119484141e5b1ef07e93b72d6ab1a5a82b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.36.0",
      "date": "2026-05-29T08:19:52.000Z",
      "distro": "noble",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "b1b304718b9b93aafb8f23e42a0dcf67bdbac4ee1cb0a349aec23560dfbbd1c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.36.0",
      "date": "2026-05-29T10:16:23.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "8f0f6a754cdbae030257017934e8456b5c9136840f8ed525694a6e4cdf6c91bd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.36.0",
      "date": "2026-05-29T10:16:58.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "a01840f935f1e3604ece30fb1f1af0aed748532097d5a117a13c68dc2693efe9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.36.0",
      "date": "2026-05-29T08:19:03.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "b2773686aae256680f1693f95ef56f1c12fb7a60d81847bfe7c2c74b62470ee6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-05-29T08:18:17.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "59fdc5d0f93112d4bfe0131c8ec0fb0d0a539fd726208d1edef095b4650123ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-05-29T08:17:46.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "c0d9df35b98bb3f711b24bf03733ade33f616041abeaba676627489c97c7e39a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.36.0",
      "date": "2026-05-29T08:18:01.000Z",
      "commit": "a6d6d14bcb4e34c69f042be91d01e400585c71bd",
      "fileid": "36106905cc29d85f83869aaf847240e74bb093db768225d5045f90d94e0b05b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626031468"
    }
  ]
}