{
  "_id": "6a1f353bb401979e7342861b",
  "Package": "augere.screen",
  "Version": "0.99.2",
  "Date": "2026-04-12",
  "Title": "Automatic Generation of Functional Screen Analyses",
  "Description": "Implements pipelines for generating functional screen\nanalysis reports in the augere framework. This uses voom to\ntest for differential abundance of barcodes with consolidation\ninto gene-level statistics. Each pipeline function generates a\nself-contained Rmarkdown report with all of the steps required\nto reproduce the analysis.",
  "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"cre\", \"aut\"), email=\"infinite.monkeys.with.keyboards@gmail.com\", comment=c(ORCID=\"0000-0002-3564-4813\"))",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/augere-bioinfo/augere.screen",
  "BugReports": "https://github.com/augere-bioinfo/augere.screen/issues",
  "biocViews": "WorkflowManagement, ReportWriting, GeneTarget,\nFunctionalGenomics",
  "Config/pak/sysreqs": "libssl-dev libnode-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-14 22:30:59 UTC",
  "RemoteUrl": "https://github.com/bioc/augere.screen",
  "RemoteRef": "HEAD",
  "RemoteSha": "295a1bd64f84a65e9730d5453caf003e191324a4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 06:34:41 UTC",
    "User": "root"
  },
  "Author": "Aaron Lun [cre, aut] (ORCID: <https://orcid.org/0000-0002-3564-4813>)",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
  "MD5sum": "efe59c115b9ae5c1a1c9420ad81ed0a6",
  "_user": "bioc",
  "_type": "src",
  "_file": "augere.screen_0.99.2.tar.gz",
  "_fileid": "a3f31781ed6c2c535361574bae190e78ecd391b89a00550fb52bb1e5a1abe1d4",
  "_filesize": 147418,
  "_sha256": "a3f31781ed6c2c535361574bae190e78ecd391b89a00550fb52bb1e5a1abe1d4",
  "_created": "2026-05-15T06:34:41.000Z",
  "_published": "2026-06-02T19:55:39.098Z",
  "_jobs": [
    {
      "job": 79159508935,
      "time": 179,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7011530668"
    },
    {
      "job": 79159508514,
      "time": 327,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7011562032"
    },
    {
      "job": 79159508280,
      "time": 335,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7011563766"
    },
    {
      "job": 79159508623,
      "time": 146,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7011544645"
    },
    {
      "job": 79159508508,
      "time": 192,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7011592327"
    },
    {
      "job": 79159508133,
      "time": 267,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7011491789"
    },
    {
      "job": 79159507652,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7368327866"
    },
    {
      "job": 79159508206,
      "time": 208,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7011536819"
    },
    {
      "job": 79159508462,
      "time": 218,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7011539423"
    },
    {
      "job": 79159508272,
      "time": 220,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7011539310"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 4
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/augere.screen",
  "_commit": {
    "id": "295a1bd64f84a65e9730d5453caf003e191324a4",
    "author": "LTLA <infinite.monkeys.with.keyboards@gmail.com>",
    "committer": "LTLA <infinite.monkeys.with.keyboards@gmail.com>",
    "message": "Added links to the BioC build status.\n",
    "time": 1778797859
  },
  "_maintainer": {
    "name": "Aaron Lun",
    "email": "infinite.monkeys.with.keyboards@gmail.com",
    "login": "ltla",
    "orcid": "0000-0002-3564-4813",
    "twitter": "@realAaronLun",
    "uuid": 8166669
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "metapod",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "augere.core",
      "role": "Imports"
    },
    {
      "package": "augere.de",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-47",
      "n": 9
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-20",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.2",
      "bioc": "3.24"
    }
  ],
  "_topics": [
    "workflowmanagement",
    "reportwriting",
    "genetarget",
    "functionalgenomics"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ltla",
      "count": 13,
      "uuid": 8166669
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 31,
    "source": "https://www.bioconductor.org/packages/stats/bioc/augere.screen"
  },
  "_devurl": "https://github.com/augere-bioinfo/augere.screen",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/augere.screen.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/augere-bioinfo/augere.screen",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "readResult",
    "runScreen",
    "wrapInput"
  ],
  "_help": [
    {
      "page": "augere.screen-package",
      "title": "augere.screen: Automatic Generation of Functional Screen Analyses",
      "topics": [
        "augere.screen-package",
        "augere.screen"
      ]
    },
    {
      "page": "runScreen",
      "title": "Differential abundance for functional screens",
      "topics": [
        "runScreen"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/augere.screen/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "alabaster.base",
    "alabaster.matrix",
    "alabaster.ranges",
    "alabaster.schemas",
    "alabaster.se",
    "assorthead",
    "augere.core",
    "augere.de",
    "Biobase",
    "BiocGenerics",
    "biocmake",
    "curl",
    "DelayedArray",
    "dir.expiry",
    "edgeR",
    "filelock",
    "generics",
    "GenomicRanges",
    "h5mread",
    "HDF5Array",
    "IRanges",
    "jsonlite",
    "jsonvalidate",
    "lattice",
    "limma",
    "locfit",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "metapod",
    "R6",
    "Rcpp",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "V8",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "userguide.Rmd",
      "filename": "userguide.html",
      "title": "Differential barcode abundance for functional screens",
      "author": "Aaron Lun, Jean-Philippe Fortin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Quick start",
        "Explaining parameters",
        "Gene-level statistics",
        "More output options",
        "Session information"
      ],
      "created": "2025-11-23 21:03:59",
      "modified": "2026-01-09 05:38:04",
      "commits": 2
    }
  ],
  "_score": 4.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "augere.screen",
  "_universes": [
    "bioc",
    "ltla",
    "augere-bioinfo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.2",
      "date": "2026-05-15T06:38:13.000Z",
      "distro": "noble",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "8bd436ab1d1d58837e9efa271823d5d11fb6d12744d48869a13d8fb37faa4636",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.2",
      "date": "2026-05-15T06:38:27.000Z",
      "distro": "noble",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "ff1c22e71259216a95b68f3516b2bd5f17101d616664ef72b2bd53041c7905db",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.2",
      "date": "2026-05-15T06:38:05.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "76bae34932da521a22c69e6895eb58cbaa323db25a0af86edf9b652b5f976ca3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.2",
      "date": "2026-05-15T06:41:19.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "061790aaffae9171e0aae10f213b062ffbbc1bdb83d92296e587ca776d371ccc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.2",
      "date": "2026-05-15T06:36:14.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "e3209cfde93fcb816f1b5183ec1a06241a13b62e45a77179ecf9cefb6aa431a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.2",
      "date": "2026-05-15T06:36:27.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "e461313c96d20bb4f61283fc8ff797c3a1ff64d37e078350951e0f272fb82e73",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.2",
      "date": "2026-05-15T06:36:27.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "876fc3d78faabeca23d5f439ec7667e234d724aad8b350746f2e890adb7c27b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.2",
      "date": "2026-06-02T19:55:13.000Z",
      "commit": "295a1bd64f84a65e9730d5453caf003e191324a4",
      "fileid": "07d59c95270ccffeb9b28ec5f13d9dbed7b0db9eb2ee172f4d3d2cfae3b93047",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25903985569"
    }
  ]
}