{
  "_id": "6ae77578818c9e3ef6dbc313",
  "Package": "roar",
  "Type": "Package",
  "Title": "Identify differential APA usage from RNA-seq alignments",
  "Version": "1.49.0",
  "Date": "2016-03-21",
  "Author": "Elena Grassi",
  "Maintainer": "Elena Grassi <grassi.e@gmail.com>",
  "Description": "Identify preferential usage of APA sites, comparing two\nbiological conditions, starting from known alternative sites\nand alignments obtained from standard RNA-seq experiments.",
  "biocViews": "Sequencing, HighThroughputSequencing, RNAseq, Transcription",
  "License": "GPL-3",
  "URL": "https://github.com/vodkatad/roar/",
  "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 12:38:30 UTC",
  "RemoteUrl": "https://github.com/bioc/roar",
  "RemoteRef": "HEAD",
  "RemoteSha": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 14:15:32 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "roar_1.49.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/76072f89cfe106d969abd7cef13c548dea6f32aec04287a7160e53473220b656",
  "_filesize": 922847,
  "_sha256": "76072f89cfe106d969abd7cef13c548dea6f32aec04287a7160e53473220b656",
  "_expires": "2027-02-09T17:23:02.000Z",
  "_created": "2026-11-01T14:15:32.000Z",
  "_published": "2026-11-01T17:23:04.151Z",
  "_upstream": "https://github.com/bioc/roar",
  "_status": "success",
  "_maintainer": {
    "name": "Elena Grassi",
    "email": "grassi.e@gmail.com",
    "login": "vodkatad",
    "description": "",
    "uuid": 1659933
  },
  "_jobs": [
    {
      "job": 124874138308,
      "time": 160,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13087906479"
    },
    {
      "job": 124874138332,
      "time": 347,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13087697443"
    },
    {
      "job": 124874138311,
      "time": 354,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13088225585"
    },
    {
      "job": 124874138340,
      "time": 295,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13093141364"
    },
    {
      "job": 124874138325,
      "time": 284,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13093641032"
    },
    {
      "job": 124866590668,
      "time": 334,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13087430955"
    },
    {
      "job": 124874138357,
      "time": 132,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13088000691"
    },
    {
      "job": 124874138375,
      "time": 276,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13086833114"
    },
    {
      "job": 124874138386,
      "time": 273,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13086843310"
    },
    {
      "job": 124874138376,
      "time": 243,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13086704190"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635",
  "_commit": {
    "id": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
    "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": 1777379910
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "version": ">= 0.99.4",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "RNAseqData.HNRNPC.bam.chr14",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "sequencing",
    "highthroughputsequencing",
    "rnaseq",
    "transcription"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "vodkatad",
      "count": 41,
      "uuid": 1659933
    },
    {
      "user": "dtenenba",
      "count": 10,
      "uuid": 2286826
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 3,
      "uuid": 8810451
    },
    {
      "user": "sonali-bioc",
      "count": 2,
      "uuid": 6373953
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 688,
    "source": "https://www.bioconductor.org/packages/stats/bioc/roar"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/vodkatad/roar",
  "_searchresults": 16,
  "_abi": {
    "exports": [
      {
        "key": "roar::ApaFragmentPrePost",
        "hash": "cbcc9d1ab3b80ef0"
      },
      {
        "key": "roar::RoarDataset",
        "hash": "d63dc6e77c39d6bd"
      },
      {
        "key": "roar::RoarDatasetMultipleAPA",
        "hash": "ea09063efac37da1"
      },
      {
        "key": "roar::generic:computePairedPvals",
        "hash": "212e628305034cda"
      },
      {
        "key": "roar::generic:computePvals",
        "hash": "bf00da40f8715aab"
      },
      {
        "key": "roar::generic:computeRoars",
        "hash": "c57fd6f7f3542b60"
      },
      {
        "key": "roar::generic:cores",
        "hash": "a3ccfeccda614f50"
      },
      {
        "key": "roar::generic:countPrePost",
        "hash": "4c45678a72a80e34"
      },
      {
        "key": "roar::generic:countResults",
        "hash": "ba034d1aa5450e6a"
      },
      {
        "key": "roar::generic:fpkmResults",
        "hash": "6810b34d8cad4946"
      },
      {
        "key": "roar::generic:generateRoarsMultipleBam",
        "hash": "fdeef8da57a9d30f"
      },
      {
        "key": "roar::generic:generateRoarsSingleBam",
        "hash": "2db363a0d0fa00b0"
      },
      {
        "key": "roar::generic:pvalueCorrectFilter",
        "hash": "668b3859865cdc44"
      },
      {
        "key": "roar::generic:pvalueFilter",
        "hash": "fc27ed2b55665802"
      },
      {
        "key": "roar::generic:standardFilter",
        "hash": "45193a925f2ab5bc"
      },
      {
        "key": "roar::generic:sumRoarCounts",
        "hash": "77946a602e239db0"
      },
      {
        "key": "roar::generic:totalResults",
        "hash": "72a81b0e17b6664a"
      }
    ],
    "imports": [
      {
        "key": "S4Vectors::Annotated",
        "hash": "9b5b8ee6ad9969f8"
      },
      {
        "key": "S4Vectors::RectangularData",
        "hash": "d414a10823a4aada"
      },
      {
        "key": "S4Vectors::Vector",
        "hash": "09cab0bd77ae353b"
      },
      {
        "key": "S4Vectors::vector_OR_Vector",
        "hash": "f3fc18c9f8ff2633"
      },
      {
        "key": "SummarizedExperiment::RangedSummarizedExperiment",
        "hash": "f15c4460724886cc"
      },
      {
        "key": "SummarizedExperiment::SummarizedExperiment",
        "hash": "d53ca73257d1e8cf"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/roar.html"
  ],
  "_homeurl": "https://github.com/vodkatad/roar",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "computePairedPvals",
    "computePvals",
    "computeRoars",
    "countPrePost",
    "countResults",
    "fpkmResults",
    "pvalueCorrectFilter",
    "pvalueFilter",
    "RoarDataset",
    "RoarDatasetFromFiles",
    "RoarDatasetMultipleAPA",
    "RoarDatasetMultipleAPAFromFiles",
    "standardFilter",
    "totalResults"
  ],
  "_help": [
    {
      "page": "roar-package",
      "title": "Identify differential APA usage from RNA-seq alignments",
      "topics": [
        "roar-package",
        "roar"
      ]
    },
    {
      "page": "checkStep-method",
      "title": "Private/inner/helper method to check the order of the invoked analysis methods",
      "topics": [
        "checkStep"
      ]
    },
    {
      "page": "combineFisherMethod-method",
      "title": "Private/inner/helper method to combine pvalues of independent test with the Fisher method",
      "topics": [
        "combineFisherMethod"
      ]
    },
    {
      "page": "computePairedPvals-method",
      "title": "Computes pvalues (Fisher test) on the read counts in this roar analysis",
      "topics": [
        "computePairedPvals",
        "computePairedPvals, RoarDataset",
        "computePairedPvals, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "computePvals-method",
      "title": "Computes pvalues (Fisher test) on the read counts in this roar analysis",
      "topics": [
        "computePvals",
        "computePvals, RoarDataset",
        "computePvals, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "computeRoars-method",
      "title": "Computes m/M and roar values",
      "topics": [
        "computeRoars",
        "computeRoars, RoarDataset, numeric, numeric",
        "computeRoars, RoarDatasetMultipleAPA, numeric, numeric"
      ]
    },
    {
      "page": "cores-method",
      "title": "Method to check how many cores are used by a roar analysis - right now not useful",
      "topics": [
        "cores"
      ]
    },
    {
      "page": "countPrePost-method",
      "title": "Counts reads falling over PRE/POST portions of the given transcripts",
      "topics": [
        "countPrePost",
        "countPrePost,RoarDataset,logical",
        "countPrePost,RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "countResults-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "countResults",
        "countResults, RoarDataset",
        "countResults, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "fpkmResults-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "fpkmResults",
        "fpkmResults, RoarDataset",
        "fpkmResults, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "getFisher-method",
      "title": "Private/inner/helper method to perform Fisher test",
      "topics": [
        "getFisher"
      ]
    },
    {
      "page": "meanAcrossAssays-method",
      "title": "Private/inner/helper method to get average counts across samples",
      "topics": [
        "meanAcrossAssays"
      ]
    },
    {
      "page": "pvalueCorrectFilter-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "pvalueCorrectFilter",
        "pvalueCorrectFilter, RoarDataset",
        "pvalueCorrectFilter, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "pvalueFilter-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "pvalueFilter",
        "pvalueFilter, RoarDataset",
        "pvalueFilter, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "RoarDataset-constructor",
      "title": "Creates a 'RoarDataset' object",
      "topics": [
        "RoarDataset"
      ]
    },
    {
      "page": "RoarDataset-class",
      "title": "Class '\"RoarDataset\"'",
      "topics": [
        "computePairedPvals,RoarDataset,numeric,numeric-method",
        "computePvals,RoarDataset-method",
        "computeRoars,RoarDataset-method",
        "cores,RoarDataset-method",
        "countPrePost,RoarDataset,logical-method",
        "countPrePost,RoarDataset-method",
        "countResults,RoarDataset-method",
        "fpkmResults,RoarDataset-method",
        "pvalueCorrectFilter,RoarDataset,numeric,numeric,character-method",
        "pvalueFilter,RoarDataset,numeric,numeric-method",
        "RoarDataset-class",
        "standardFilter,RoarDataset,numeric-method",
        "totalResults,RoarDataset-method"
      ]
    },
    {
      "page": "RoarDatasetFromFiles-constructor",
      "title": "Creates a 'RoarDataset' object",
      "topics": [
        "RoarDatasetFromFiles"
      ]
    },
    {
      "page": "RoarDatasetMultipleAPA-constructor",
      "title": "Creates a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "RoarDatasetMultipleAPA-class",
      "title": "Class '\"RoarDatasetMultipleAPA\"'",
      "topics": [
        "computePairedPvals,RoarDatasetMultipleAPA,numeric,numeric-method",
        "computePvals,RoarDatasetMultipleAPA-method",
        "computeRoars,RoarDatasetMultipleAPA-method",
        "cores,RoarDatasetMultipleAPA-method",
        "countPrePost,RoarDatasetMultipleAPA,logical-method",
        "countPrePost,RoarDatasetMultipleAPA-method",
        "countResults,RoarDatasetMultipleAPA-method",
        "fpkmResults,RoarDatasetMultipleAPA-method",
        "pvalueCorrectFilter,RoarDatasetMultipleAPA,numeric,numeric,character-method",
        "pvalueFilter,RoarDatasetMultipleAPA,numeric,numeric-method",
        "RoarDatasetMultipleAPA-class",
        "standardFilter,RoarDatasetMultipleAPA,numeric-method",
        "totalResults,RoarDatasetMultipleAPA-method"
      ]
    },
    {
      "page": "RoarDatasetMultipleAPAFromFiles-constructor",
      "title": "Creates a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "RoarDatasetMultipleAPAFromFiles"
      ]
    },
    {
      "page": "standardFilter-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "standardFilter",
        "standardFilter, RoarDataset",
        "standardFilter, RoarDatasetMultipleAPA"
      ]
    },
    {
      "page": "totalResults-method",
      "title": "Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object",
      "topics": [
        "totalResults",
        "totalResults, RoarDataset",
        "totalResults, RoarDatasetMultipleAPA"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "UCSC.utils",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "roar.Rnw",
      "filename": "roar.pdf",
      "title": "Identify differential APA usage from RNA-seq alignments",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Input data",
        "Analysis steps",
        "Appendix"
      ],
      "created": "2013-12-19 23:25:31",
      "modified": "2017-11-27 06:20:44",
      "commits": 9
    }
  ],
  "_score": 5.107209969647869,
  "_indexed": true,
  "_nocasepkg": "roar",
  "_universes": [
    "bioc",
    "vodkatad"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-11-01T14:38:06.000Z",
      "distro": "resolute",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/1702c94f275646ef8257c4ef9aa85a8b4f11244512cc1344e6790e8c3e86e16b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.49.0",
      "date": "2026-11-01T14:37:27.000Z",
      "distro": "resolute",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/36fa5b07235cb3caecc424a5a5ff38524e6250e73e793e819ab06b3f5f2f9a62",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-11-01T17:18:27.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/8eabb682bfaf6bc4c642a5105a06a9c10e40fb44e178cf19accc23d4e5da1f77",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.49.0",
      "date": "2026-11-01T17:18:02.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/f28011c3621d0e6930bcac0b5e084a3db20622492ecce82381fad292e837843f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.49.0",
      "date": "2026-11-01T14:36:40.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/e709ccf2e1f935f4992d6ef8d69a9c431a167e36bf14d623f4dbb5f48dee447f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-11-01T14:19:32.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/3ff7eccce9f01c030c29c687bbd72c69dc3121bcea384f274ba5f044732eb787",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-11-01T14:19:47.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/95e942afef0e653bf27fc2c54bedbf8be7a0dcb1ecd43f8353098add0108cac1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.49.0",
      "date": "2026-11-01T14:19:36.000Z",
      "commit": "ea42a9ed2448f14c89582dd14e6bc9be5492bcb3",
      "fileid": "https://r2.ropensci.org/bee51ea5f31112b3e4bf4276ab70327ef601eb0e3092a4d6136d4511b185e186",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310601635"
    }
  ]
}