{
  "_id": "6a61d20b768d0b54cfc790a4",
  "Package": "Rbowtie",
  "Type": "Package",
  "Title": "R bowtie wrapper",
  "Version": "1.53.0",
  "Date": "2023-01-29",
  "Authors@R": "c(person(\"Florian\", \"Hahne\", role = c(\"aut\")),\nperson(\"Anita\", \"Lerch\", role = c(\"aut\")),\nperson(\"Michael\", \"Stadler\", role = c(\"aut\", \"cre\"),\nemail = \"michael.stadler@fmi.ch\",\ncomment = c(ORCID = \"0000-0002-2269-4934\")))",
  "Maintainer": "Michael Stadler <michael.stadler@fmi.ch>",
  "SystemRequirements": "GNU make",
  "Description": "This package provides an R wrapper around the popular\nbowtie short read aligner and around SpliceMap, a de novo\nsplice junction discovery and alignment tool. The package is\nused by the QuasR bioconductor package. We recommend to use the\nQuasR package instead of using Rbowtie directly.",
  "License": "Artistic-2.0 | file LICENSE",
  "LazyLoad": "yes",
  "URL": "https://github.com/fmicompbio/Rbowtie",
  "BugReports": "https://github.com/fmicompbio/Rbowtie/issues",
  "biocViews": "Sequencing, Alignment",
  "Archs": "x64",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:11 UTC",
  "RemoteUrl": "https://github.com/bioc/Rbowtie",
  "RemoteRef": "HEAD",
  "RemoteSha": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-23 08:19:52 UTC",
    "User": "root"
  },
  "Author": "Florian Hahne [aut],\nAnita Lerch [aut],\nMichael Stadler [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2269-4934>)",
  "_user": "bioc",
  "_type": "src",
  "_file": "Rbowtie_1.53.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7fa1ed8708091764b5fe4950d90210288e2f263a01174338ed974a3c30fe666c",
  "_filesize": 760816,
  "_sha256": "7fa1ed8708091764b5fe4950d90210288e2f263a01174338ed974a3c30fe666c",
  "_expires": "2026-10-31T08:34:17.000Z",
  "_created": "2026-07-23T08:19:52.000Z",
  "_published": "2026-07-23T08:34:19.132Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985",
  "_status": "success",
  "_upstream": "https://github.com/bioc/Rbowtie",
  "_commit": {
    "id": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
    "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": 1777379831
  },
  "_maintainer": {
    "name": "Michael Stadler",
    "email": "michael.stadler@fmi.ch",
    "login": "mbstadler",
    "orcid": "0000-0002-2269-4934",
    "description": "",
    "uuid": 13657342
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 89153392289,
      "time": 219,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8557090724"
    },
    {
      "job": 89153392380,
      "time": 154,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8557069436"
    },
    {
      "job": 89153392349,
      "time": 194,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8557082765"
    },
    {
      "job": 89153392350,
      "time": 167,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8557073626"
    },
    {
      "job": 89153392377,
      "time": 207,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8557086394"
    },
    {
      "job": 89153392391,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8557201093"
    },
    {
      "job": 89153392353,
      "time": 255,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8557223891"
    },
    {
      "job": 89153392384,
      "time": 106,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8557188019"
    },
    {
      "job": 89153392347,
      "time": 339,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8557257100"
    },
    {
      "job": 89152471872,
      "time": 349,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8557017011"
    },
    {
      "job": 89153392307,
      "time": 99,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 89153392332,
      "time": 162,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8557072338"
    },
    {
      "job": 89153392366,
      "time": 181,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8557077980"
    },
    {
      "job": 89153392355,
      "time": 170,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8557075332"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.53.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.52.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "alignment"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "mbstadler",
      "count": 113,
      "uuid": 13657342
    },
    {
      "user": "dtenenba",
      "count": 23,
      "uuid": 2286826
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 3,
      "uuid": 8810451
    },
    {
      "user": "mtmorgan",
      "count": 2,
      "uuid": 118552
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "csoneson",
      "count": 1,
      "uuid": 5628952
    },
    {
      "user": "sonali-bioc",
      "count": 1,
      "uuid": 6373953
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 450,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 834,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Rbowtie"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/fmicompbio/rbowtie",
  "_searchresults": 25,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Rbowtie.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/fmicompbio/rbowtie",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bowtie",
    "bowtie_build",
    "bowtie_build_usage",
    "bowtie_usage",
    "bowtie_version",
    "SpliceMap"
  ],
  "_help": [
    {
      "page": "Rbowtie-package",
      "title": "R bowtie wrapper",
      "topics": [
        "Rbowtie-package",
        "Rbowtie"
      ]
    },
    {
      "page": "Rbowtie",
      "title": "Interface to bowtie",
      "topics": [
        "bowtie",
        "bowtie_build",
        "bowtie_build_usage",
        "bowtie_usage",
        "bowtie_version"
      ]
    },
    {
      "page": "SpliceMap",
      "title": "Interface to SpliceMap",
      "topics": [
        "SpliceMap"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Rbowtie/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "Rbowtie-Overview.Rmd",
      "filename": "Rbowtie-Overview.html",
      "title": "An introduction to Rbowtie",
      "author": "Michael Stadler, Dimos Gaidatzis, Anita Lerch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Preliminaries",
        "Citing Rbowtie",
        "Installation",
        "Loading of Rbowtie",
        "How to get help",
        "Example usage for individual Rbowtie functions",
        "Build the reference index with bowtie_build",
        "Create alignment with bowtie",
        "Create spliced alignment with SpliceMap",
        "Session information",
        "References"
      ],
      "created": "2018-01-06 14:42:44",
      "modified": "2018-07-19 09:28:50",
      "commits": 4
    }
  ],
  "_score": 6.623249290397901,
  "_indexed": true,
  "_nocasepkg": "rbowtie",
  "_universes": [
    "bioc",
    "mbstadler",
    "fmicompbio"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-07-23T08:22:57.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/4ebf436c691ea39187b19013dcbde6c5bbb60d956d838c4a0c9591d70b37d0d3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-07-23T08:23:32.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/6e43c6ec9ca439044d3ee6f2553e60296cb483abab6105232aa8a7c14df784bb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-07-23T08:22:57.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/f92f26c00687d66294e0b0b274586817bce412428ba94ae0504e4ea1232c9d34",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.53.0",
      "date": "2026-07-23T08:23:42.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/e01fd904765c362631a6f7b879edf3cf974732b1222a709985c2839398d9422a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-07-23T08:30:04.000Z",
      "arch": "aarch64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/4cec459f0790870e9d5eca86b6d85f1e3c56ac4a889e930419d20c7725f9d26b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-07-23T08:30:26.000Z",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/0d6eb1d2d833b198526581ed4b6dc12fd7a51c16c94617aa67422289b87bff77",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-07-23T08:29:26.000Z",
      "arch": "aarch64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/c410f381ef940778e8b949de5ebd7ca865d04e24747b477d02c9e502702f744f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.53.0",
      "date": "2026-07-23T08:31:30.000Z",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/5e94fe3c03f52c056d31ac04af02ee01d607f64ec60ba5b4647a05fb8c62accf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-07-23T08:22:28.000Z",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/9a9df25419c9d13913db1aaa19ed7ec5b87a05e3f8f2a2c71c1c0efb2ff89ee5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-07-23T08:22:28.000Z",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/0322498cf267f26e4d5ad5119302136e92b1a58046a85e0189e5509bc65f9e6f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.53.0",
      "date": "2026-07-23T08:22:30.000Z",
      "arch": "x86_64",
      "commit": "7fc4e20ff1a0ba98704abb42e60eaa2b64baf2ac",
      "fileid": "https://r2.ropensci.org/d5b896ea613dcc8eb66b097503c460ef5deb2d8af8c0d6fd45b3b7e57997cb9c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29990641985"
    }
  ]
}