{
  "_id": "6a1f06fbb401979e7341bd7c",
  "Package": "tidyCoverage",
  "Title": "Extract and aggregate genomic coverage over features of interest",
  "Version": "1.9.0",
  "Date": "2023-11-09",
  "Authors@R": "person(\"Jacques\", \"Serizay\", , \"jacquesserizay@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "`tidyCoverage` framework enables tidy manipulation of\ncollections of genomic tracks and features using\n`tidySummarizedExperiment` methods. It facilitates the\nextraction, aggregation and visualization of genomic coverage\nover individual or thousands of genomic loci, relying on\n`CoverageExperiment` and `AggregatedCoverage` classes. This\naccelerates the integration of genomic track data in genomic\nanalysis workflows.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/js2264/tidyCoverage",
  "BugReports": "https://github.com/js2264/tidyCoverage/issues",
  "biocViews": "Software, Sequencing, Coverage,",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "LazyData": "false",
  "Config/pak/sysreqs": "libcairo2-dev libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libtiff-dev libwebp-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:13 UTC",
  "RemoteUrl": "https://github.com/bioc/tidyCoverage",
  "RemoteRef": "HEAD",
  "RemoteSha": "c3c722da2b18433b98a2e998501cf085fada7685",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 10:11:21 UTC",
    "User": "root"
  },
  "Author": "Jacques Serizay [aut, cre]",
  "Maintainer": "Jacques Serizay <jacquesserizay@gmail.com>",
  "MD5sum": "3888df822c227ae29e325ac3dd2ffa6f",
  "_user": "bioc",
  "_type": "src",
  "_file": "tidyCoverage_1.9.0.tar.gz",
  "_fileid": "00e7b8f3b5345e055dbeb4018c1201d236231da844084bf6eb5e2a96b034ddce",
  "_filesize": 3746582,
  "_sha256": "00e7b8f3b5345e055dbeb4018c1201d236231da844084bf6eb5e2a96b034ddce",
  "_created": "2026-05-15T10:11:21.000Z",
  "_published": "2026-06-02T16:38:19.250Z",
  "_jobs": [
    {
      "job": 79122158501,
      "time": 225,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014868863"
    },
    {
      "job": 79122158895,
      "time": 497,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014943509"
    },
    {
      "job": 79122159121,
      "time": 514,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014949891"
    },
    {
      "job": 79122158692,
      "time": 257,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014948731"
    },
    {
      "job": 79122158734,
      "time": 219,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014935566"
    },
    {
      "job": 79122158462,
      "time": 431,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014804368"
    },
    {
      "job": 79122157860,
      "time": 203,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7363980488"
    },
    {
      "job": 79122159281,
      "time": 356,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7051462083"
    },
    {
      "job": 79122159360,
      "time": 333,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7051456946"
    },
    {
      "job": 79122158950,
      "time": 331,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7051455267"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/tidyCoverage",
  "_commit": {
    "id": "c3c722da2b18433b98a2e998501cf085fada7685",
    "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": 1777381333
  },
  "_maintainer": {
    "name": "Jacques Serizay",
    "email": "jacquesserizay@gmail.com",
    "login": "js2264",
    "uuid": 19528818
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocIO",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrastr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "fansi",
      "role": "Imports"
    },
    {
      "package": "pillar",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "vctrs",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidySummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "plyranges",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Mmusculus.UCSC.mm10.knownGene",
      "role": "Suggests"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "hues",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-51",
      "n": 6
    },
    {
      "week": "2025-52",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "sequencing",
    "coverage"
  ],
  "_stars": 24,
  "_contributors": [
    {
      "user": "js2264",
      "count": 68,
      "uuid": 19528818
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 258,
    "source": "https://www.bioconductor.org/packages/stats/bioc/tidyCoverage"
  },
  "_devurl": "https://github.com/js2264/tidycoverage",
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/tidyCoverage.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/js2264/tidycoverage",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggregate",
    "coarsen",
    "CoverageExperiment",
    "geom_aggrcoverage",
    "geom_coverage",
    "scale_x_genome",
    "scale_y_coverage",
    "show"
  ],
  "_datasets": [
    {
      "name": "ac",
      "title": "Example 'CoverageExperiment' and 'AggregatedCoverage' objects",
      "object": "ac",
      "file": "ac.rda",
      "class": [
        "AggregatedCoverage"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ce",
      "title": "Example 'CoverageExperiment' and 'AggregatedCoverage' objects",
      "object": "ce",
      "file": "ce.rda",
      "class": [
        "CoverageExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AggregatedCoverage",
      "title": "aggregate",
      "topics": [
        "aggregate,CoverageExperiment-method",
        "AggregatedCoverage"
      ]
    },
    {
      "page": "as_tibble-AggregatedCoverage",
      "title": "as_tibble",
      "topics": [
        "as_tibble-AggregatedCoverage",
        "as_tibble.AggregatedCoverage"
      ]
    },
    {
      "page": "CoverageExperiment",
      "title": "CoverageExperiment",
      "topics": [
        "coarsen",
        "coarsen,CoverageExperiment-method",
        "CoverageExperiment",
        "CoverageExperiment,BigWigFile,GRanges-method",
        "CoverageExperiment,BigWigFile,GRangesList-method",
        "CoverageExperiment,BigWigFile,list-method",
        "CoverageExperiment,BigWigFileList,GRanges-method",
        "CoverageExperiment,BigWigFileList,GRangesList-method",
        "CoverageExperiment,BigWigFileList,list-method",
        "CoverageExperiment,list,GRanges-method",
        "CoverageExperiment,list,GRangesList-method",
        "CoverageExperiment,list,list-method",
        "CoverageExperiment,RleList,GRanges-method",
        "CoverageExperiment,RleList,GRangesList-method",
        "CoverageExperiment,RleList,list-method"
      ]
    },
    {
      "page": "data",
      "title": "Example 'CoverageExperiment' and 'AggregatedCoverage' objects",
      "topics": [
        "ac",
        "ce",
        "data"
      ]
    },
    {
      "page": "expand-CoverageExperiment",
      "title": "Expand a CoverageExperiment object",
      "topics": [
        "expand-CoverageExperiment",
        "expand.CoverageExperiment"
      ]
    },
    {
      "page": "ggplot-tidyCoverage",
      "title": "Plotting functions",
      "topics": [
        "geom_aggrcoverage",
        "geom_coverage",
        "ggplot-tidyCoverage",
        "scale_x_genome",
        "scale_y_coverage"
      ]
    },
    {
      "page": "show-tidyCoverage",
      "title": "show method for 'CoverageExperiment' and 'AggregatedCoverage' objects",
      "topics": [
        "show,AggregatedCoverage-method",
        "show,CoverageExperiment-method",
        "show-tidyCoverage"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/tidyCoverage/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "Cairo",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "dplyr",
    "fansi",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrastr",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "ragg",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "vipor",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "tidyCoverage.Rmd",
      "filename": "tidyCoverage.html",
      "title": "Introduction to tidyCoverage",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "CoverageExperiment and AggregatedCoverage classes",
        "CoverageExperiment",
        "AggregatedCoverage",
        "Manipulate CoverageExperiment objects",
        "Create a CoverageExperiment object",
        "Bin a CoverageExperiment object",
        "Expand a CoverageExperiment object",
        "Plot coverage of a set of tracks over a single genomic locus",
        "Manipulate AggregatedCoverage objects",
        "Aggregate a CoverageExperiment into an AggregatedCoverage object",
        "AggregatedCoverage over multiple tracks / feature sets",
        "Plot aggregated coverages with ggplot2",
        "Use a tidy grammar",
        "Example workflow using tidy grammar",
        "Example use case: AnnotationHub and TxDb resources",
        "Recover TSSs of forward mouse genes",
        "Recover H3K4me3 coverage track from AnnotationHub",
        "Compute the aggregated coverage of H3K4me3 ± 3kb around the TSSs of forward mouse genes",
        "With more genomic tracks",
        "Session info"
      ],
      "created": "2023-11-27 13:23:34",
      "modified": "2025-12-20 15:50:43",
      "commits": 15
    }
  ],
  "_score": 5.778151250383644,
  "_indexed": true,
  "_nocasepkg": "tidycoverage",
  "_universes": [
    "bioc",
    "js2264"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-15T10:16:23.000Z",
      "distro": "noble",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "1316b3428e8dc164b80d1b977bb3bce75e1b390acede145b4a9530ae17946f1b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-15T10:16:46.000Z",
      "distro": "noble",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "d5b9ea5c9d9c4f078541c2cd7d79331008b5c5a095464a3243e268fd9e29217a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-15T10:18:11.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "bde5b9f333bcd7c405fb9169d94972bd72ac2d6a742a4f2c24760fa3312c09e4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-15T10:17:44.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "8010144672890fa7f99e2410a2012ffeef5801109e66bc377c7d080667f691af",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-18T07:03:37.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "d29698c9a6b751943d8bc0fe57d15081af1f163a95209efeab7c3dfdf55a658e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-18T07:03:16.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "2410b7d935470351792899e87665d8fa259d9d4556cf3ab4843add449b76d72f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-18T07:03:18.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "84c3ee74db1bee0149e82e21a3767c1f7c1998b6a2453f34e270d78c79b364a5",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-06-02T16:37:53.000Z",
      "commit": "c3c722da2b18433b98a2e998501cf085fada7685",
      "fileid": "b267af453726f5ed4b8ae0e2e5c152ac89c8693c3bc2dca745d9cafaf1542a0f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912115966"
    }
  ]
}