{
  "_id": "6ae336a68d250e7ad09f04ef",
  "Package": "bcSeq",
  "Type": "Package",
  "Title": "Fast Sequence Mapping in High-Throughput shRNA and CRISPR\nScreens",
  "Version": "1.35.0",
  "Date": "2019-07-18",
  "Authors@R": "c(person(\"Jiaxing\",\"Lin\", role = c(\"aut\", \"cre\"), \nemail = \"jiaxing.lin@duke.edu\"),\nperson(\"Jeremy\", \"Gresham\", role = \"aut\"),\nperson(\"Jichun\", \"Xie\", role = \"aut\"),\nperson(\"Kouros\", \"Owzar\", role = \"aut\"),\nperson(\"Tongrong\", \"Wang\", role = \"ctb\"),\nperson(\"So Young\", \"Kim\", role = \"ctb\"),\nperson(\"James\", \"Alvarez\", role = \"ctb\"),\nperson(\"Jeffrey S.\", \"Damrauer\", role = \"ctb\"),\nperson(\"Scott\", \"Floyd\", role = \"ctb\"),\nperson(\"Joshua\", \"Granek\", role = \"ctb\"),\nperson(\"Andrew\", \"Allen\", role = \"ctb\"),\nperson(\"Cliburn\", \"Chan\", role = \"ctb\"))",
  "Author": "Jiaxing Lin [aut, cre], Jeremy Gresham [aut], Jichun Xie [aut],\nKouros Owzar [aut], Tongrong Wang [ctb], So Young Kim [ctb],\nJames Alvarez [ctb], Jeffrey S. Damrauer [ctb], Scott Floyd\n[ctb], Joshua Granek [ctb], Andrew Allen [ctb], Cliburn Chan\n[ctb]",
  "Maintainer": "Jiaxing Lin <jiaxing.lin@duke.edu>",
  "Description": "This Rcpp-based package implements a highly efficient data\nstructure and algorithm for performing alignment of short reads\nfrom CRISPR or shRNA screens to reference barcode library.\nSequencing error are considered and matching qualities are\nevaluated based on Phred scores. A Bayes' classifier is\nemployed to predict the originating barcode of a read. The\npackage supports provision of user-defined probability models\nfor evaluating matching qualities. The package also supports\nmulti-threading.",
  "License": "GPL (>= 2)",
  "biocViews": "ImmunoOncology, Alignment, CRISPR, Sequencing,\nSequenceMatching, MultipleSequenceAlignment, Software, ATACSeq",
  "URL": "https://github.com/jl354/bcSeq",
  "BugReports": "https://support.bioconductor.org",
  "VignetteBuilder": "knitr",
  "BuildVignettes": "yes",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:57 UTC",
  "RemoteUrl": "https://github.com/bioc/bcSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
  "Packaged": {
    "Date": "2026-10-29 11:04:48 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "bcSeq_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/a5bc67b11a9dfc4ce943d26262a839d6b0d5dbd81f0c540e65a9c569860d4a86",
  "_filesize": 139090,
  "_sha256": "a5bc67b11a9dfc4ce943d26262a839d6b0d5dbd81f0c540e65a9c569860d4a86",
  "_expires": "2027-02-06T12:05:56.000Z",
  "_created": "2026-10-29T11:04:48.000Z",
  "_published": "2026-10-29T12:05:58.828Z",
  "_upstream": "https://github.com/bioc/bcSeq",
  "_status": "failure",
  "_maintainer": {
    "name": "Jiaxing Lin",
    "email": "jiaxing.lin@duke.edu"
  },
  "_jobs": [
    {
      "job": 123409617740,
      "time": 300,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12893060210"
    },
    {
      "job": 123409617896,
      "time": 180,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12891504080"
    },
    {
      "job": 123409617916,
      "time": 193,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12892302467"
    },
    {
      "job": 123409618213,
      "time": 305,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12892182838"
    },
    {
      "job": 123409617955,
      "time": 344,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12892442686"
    },
    {
      "job": 123409618090,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12894933549"
    },
    {
      "job": 123409618157,
      "time": 336,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12895138626"
    },
    {
      "job": 123409617957,
      "time": 153,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12895192831"
    },
    {
      "job": 123409617987,
      "time": 394,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12895397484"
    },
    {
      "job": 123406740737,
      "time": 382,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12892541128"
    },
    {
      "job": 123409617782,
      "time": 248,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12892337686"
    },
    {
      "job": 123409618088,
      "time": 249,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12892855912"
    },
    {
      "job": 123409617941,
      "time": 213,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12891803767"
    },
    {
      "job": 123409617932,
      "time": 138,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12891469826"
    },
    {
      "job": 123409617882,
      "time": 279,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12891859330"
    },
    {
      "job": 123409618036,
      "time": 410,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12892382973"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791",
  "_commit": {
    "id": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
    "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": 1777380417
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Matrix",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.12",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "alignment",
    "crispr",
    "sequencing",
    "sequencematching",
    "multiplesequencealignment",
    "software",
    "atacseq",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jl354",
      "count": 2,
      "uuid": 32273455
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 502,
    "source": "https://www.bioconductor.org/packages/stats/bioc/bcSeq"
  },
  "_devurl": "https://github.com/jl354/bcseq",
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bcSeq.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_homeurl": "https://github.com/jl354/bcseq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bcSeq_edit",
    "bcSeq_hamming",
    "trimRead",
    "uniqueBar"
  ],
  "_help": [
    {
      "page": "bcSeq-package",
      "title": "Fast Sequence Alignment for High-throughput shRNA and CRISPR Screens",
      "topics": [
        "bcSeq-package"
      ]
    },
    {
      "page": "bcSeq_edit",
      "title": "Function to perform reads to barcode alignment tolerating edit type error distance.",
      "topics": [
        "bcSeq_edit"
      ]
    },
    {
      "page": "bcSeq_hamming",
      "title": "Function to perform reads to barcode alignment tolerating hamming type error distance",
      "topics": [
        "bcSeq_hamming"
      ]
    },
    {
      "page": "trimRead",
      "title": "Tool function to trim adaptor for read sequences.",
      "topics": [
        "trimRead"
      ]
    },
    {
      "page": "uniqueBar",
      "title": "Tool function to obtain unique barcode sequences from a library .",
      "topics": [
        "uniqueBar"
      ]
    }
  ],
  "_rundeps": [
    "BiocGenerics",
    "Biostrings",
    "crayon",
    "generics",
    "IRanges",
    "lattice",
    "Matrix",
    "Rcpp",
    "S4Vectors",
    "Seqinfo",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 2.778151250383644,
  "_indexed": true,
  "_nocasepkg": "bcseq",
  "_universes": [
    "bioc",
    "jl354"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-29T11:07:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/9f040c49e0a15fc1b43f0143700a13128e631d5bc7ad34430f141ee5940e23a8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-29T11:07:55.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/ba419c7e0ae6cfe77d234480019755db1edd7b16ccfb081622a7bf063263c9e2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-29T11:09:41.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/8b183a49b1c9ec9d5225231027b2e6bce949592f346abdf77259c680f1a89358",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-29T11:10:00.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/52e28966813731eb79e0f385b6192a12446c0af6c3209d1d30516f3d0b4daf25",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-29T12:04:06.000Z",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/1b9f0322541fa2b35f148500489136c5506b7fcab80623d4506ed4fa0328c479",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-29T12:02:05.000Z",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/44ecc37245b5822e6d53063c6d42ca77d70c14a186a4b584c136c850cb17e36b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-29T12:03:31.000Z",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/cc8c7ef4b6336ceed797211b13a4da02f757e12eb4d1a2159dc61c9c42e28c84",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-29T12:02:50.000Z",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/115c0399b3621ac6c78833f66182f26b1ef21c980e85b174f6bc284b714416ce",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-10-29T11:09:29.000Z",
      "arch": "emscripten",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/cf601a7bbd983c172e61d80c088c4132bba9a239ab8227cc1903e8c647fdd183",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-29T11:08:12.000Z",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/f2259007c05dc2cb649928e62cd69a80a90e159d0497ffb8d945715d1f50e60a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-29T11:06:35.000Z",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/85b2255abebe7fd84e00b404a7d0ce64427804db9b5c966ec4466678c9edee94",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-29T11:06:26.000Z",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/6085584ae07bb972a82663f3b8cd9544dd3394b9b4307fbcc8ccd527ecae52b4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-29T11:08:49.000Z",
      "arch": "aarch64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/6856e97c9dddefb509d51dee588f143f90f70dc2c37b80069713c8a0c5674f95",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-29T11:10:30.000Z",
      "arch": "x86_64",
      "commit": "8ba61021631a4b50dc79d6ba66896ef76a9ba348",
      "fileid": "https://r2.ropensci.org/42cc8e0ff8b505ed1fb374c310f10d78b3be39448cb5cacf371e38e6d81078cc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40861784791"
    }
  ]
}