{
  "_id": "6a266c20794753ddbc3e8406",
  "Package": "geneRxCluster",
  "Date": "2013-02-13",
  "Version": "1.48.0",
  "License": "GPL (>= 2)",
  "Description": "Detect Differential Clustering of Genomic Sites such as\ngene therapy integrations.  The package provides some functions\nfor exploring genomic insertion sites originating from two\ndifferent sources. Possibly, the two sources are two different\ngene therapy vectors.  Vectors are preferred that target\nsensitive regions less frequently, motivating the search for\nlocalized clusters of insertions and comparison of the clusters\nformed by integration of different vectors.  Scan statistics\nallow the discovery of spatial differences in clustering and\ncalculation of False Discovery Rates (FDRs) providing\nstatistical methods for comparing retroviral vectors. A scan\nstatistic for comparing two vectors using multiple window\nwidths to detect clustering differentials and compute FDRs is\nimplemented here.",
  "Title": "gRx Differential Clustering",
  "Author": "Charles Berry",
  "Maintainer": "Charles Berry <ccberry@ucsd.edu>",
  "biocViews": "Sequencing, Clustering, Genetics",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:31 UTC",
  "RemoteUrl": "https://github.com/bioc/geneRxCluster",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-08 07:04:44 UTC",
    "User": "root"
  },
  "MD5sum": "6b8c0844049e8718b5a3719a13b2c898",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "geneRxCluster_1.48.0.tar.gz",
  "_fileid": "bffb7bff833f4c2250a18579e2f72f1d92366488118d8196c8cfe2bb876644e8",
  "_filesize": 259107,
  "_sha256": "bffb7bff833f4c2250a18579e2f72f1d92366488118d8196c8cfe2bb876644e8",
  "_created": "2026-06-08T07:04:44.000Z",
  "_published": "2026-06-08T07:15:44.627Z",
  "_jobs": [
    {
      "job": 80039480419,
      "time": 123,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7473561446"
    },
    {
      "job": 80039480476,
      "time": 608,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7473687941"
    },
    {
      "job": 80039480506,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7473580334"
    },
    {
      "job": 80039480440,
      "time": 151,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473569577"
    },
    {
      "job": 80039480445,
      "time": 172,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473573738"
    },
    {
      "job": 80039480463,
      "time": 132,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7473584292"
    },
    {
      "job": 80039480470,
      "time": 347,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7473629359"
    },
    {
      "job": 80039480464,
      "time": 120,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473586755"
    },
    {
      "job": 80039480436,
      "time": 257,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473600846"
    },
    {
      "job": 80038983947,
      "time": 212,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473529161"
    },
    {
      "job": 80039480468,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473557379"
    },
    {
      "job": 80039480482,
      "time": 107,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7473556912"
    },
    {
      "job": 80039480439,
      "time": 113,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7473558837"
    },
    {
      "job": 80039480446,
      "time": 201,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473581380"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/geneRxCluster",
  "_commit": {
    "id": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379911
  },
  "_maintainer": {
    "name": "Charles Berry",
    "email": "ccberry@ucsd.edu",
    "login": "chasberry",
    "description": "",
    "uuid": 1952008
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "clustering",
    "genetics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 336,
    "source": "https://www.bioconductor.org/packages/stats/bioc/geneRxCluster"
  },
  "_searchresults": 1,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/geneRxCluster.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "critVal.alpha",
    "critVal.power",
    "critVal.target",
    "gRxCluster",
    "gRxPlot",
    "gRxPlotClumps",
    "gRxSummary",
    "noprune",
    "prune.loglik"
  ],
  "_help": [
    {
      "page": "critVal.alpha",
      "title": "critical regions",
      "topics": [
        "critVal.alpha"
      ]
    },
    {
      "page": "critVal.power",
      "title": "critical regions",
      "topics": [
        "critVal.power"
      ]
    },
    {
      "page": "critVal.target",
      "title": "critical regions",
      "topics": [
        "critVal.target"
      ]
    },
    {
      "page": "geneRxCluster",
      "title": "Differential Clustering of Integration Sites",
      "topics": [
        "geneRxCluster-package",
        "geneRxCluster"
      ]
    },
    {
      "page": "gRxCluster",
      "title": "gRxCluster",
      "topics": [
        "gRxCluster"
      ]
    },
    {
      "page": "gRxCluster-object",
      "title": "gRxCluster object",
      "topics": [
        "gRxCluster-object"
      ]
    },
    {
      "page": "gRxPlot",
      "title": "gRxPlot",
      "topics": [
        "gRxPlot"
      ]
    },
    {
      "page": "gRxPlotClumps",
      "title": "gRxPlotClumps",
      "topics": [
        "gRxPlotClumps"
      ]
    },
    {
      "page": "gRxSummary",
      "title": "gRxSummary",
      "topics": [
        "gRxSummary"
      ]
    },
    {
      "page": "noprune",
      "title": "noprune",
      "topics": [
        "noprune"
      ]
    },
    {
      "page": "plot.cutpoints",
      "title": "plot.cutpoints",
      "topics": [
        "plot.cutpoints"
      ]
    },
    {
      "page": "prune.loglik",
      "title": "prune.loglik",
      "topics": [
        "prune.loglik"
      ]
    }
  ],
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "GenomicRanges",
    "IRanges",
    "S4Vectors",
    "Seqinfo"
  ],
  "_vignettes": [
    {
      "source": "tutorial.Rnw",
      "filename": "tutorial.pdf",
      "title": "Using geneRxCluster",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Basic Use",
        "Customizing Critical Regions and Filters"
      ],
      "created": "2013-12-24 23:19:41",
      "modified": "2014-02-13 20:39:35",
      "commits": 2
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": false,
  "_nocasepkg": "generxcluster",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/geneRxCluster",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-06-08T07:14:46.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "f11c4184855fff5dc0ed7b9ae3577e335820fdefbe6ac57956f71d80235c7d2d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-06-08T07:07:42.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "314d24e6a5a43f17c454af3f3e78c70e5e0affaaa4bd6fb03d7233b1b40fd173",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-06-08T07:07:07.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "75ba40450f70a42825787980d258804a184a0117b760b9811a1f0bcccf84d434",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.48.0",
      "date": "2026-06-08T07:07:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "aa504fd3cce5eddaed12a7bbaeed67fc90dfaa91be9125c1363edea373a1438d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-06-08T07:08:03.000Z",
      "arch": "aarch64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "a1ce8245d362aa06cb40836d1f69678ac066797cd376fb75d83582cc908c4a0b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-06-08T07:09:35.000Z",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "72e74276d1dca916fdbb7c9458d7a5ab82212779885f620825d8c7fb16f9b340",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-06-08T07:08:22.000Z",
      "arch": "aarch64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "95a4a7df02774df28ab563690c609d324d9687a473b1a827586ebc43d5246d0f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.48.0",
      "date": "2026-06-08T07:08:37.000Z",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "a8ff08c54668d47b44869afef5ccf241170061a849086b81c1fcbfe0ac5c6a50",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.48.0",
      "date": "2026-06-08T07:06:57.000Z",
      "arch": "emscripten",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "76083a8d1f17a905df0711927dd378d3b3932ae177ba7a2e81f6267902412024",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-06-08T07:06:00.000Z",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "b7f42218e21db9e771c36b9063626cedae22106806e4b5b94d9db4eeaf0d72cb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-06-08T07:05:55.000Z",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "1b030d8ee65296cd8f2c2bfc66ab0d1bbbf8a2fc02a6b8fce2e6d7e9a870730f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.48.0",
      "date": "2026-06-08T07:07:33.000Z",
      "arch": "x86_64",
      "commit": "dbf63d9ccb8f84c69d94478deca4af4e5cf8a7ef",
      "fileid": "8ba499c611dfdb94220f1e829d17fcc7fcb365badee716338b8f03ee76019543",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121322467"
    }
  ]
}