{
  "_id": "6a33a0723efcd9bda43a8636",
  "Package": "RSVSim",
  "Type": "Package",
  "Title": "RSVSim: an R/Bioconductor package for the simulation of\nstructural variations",
  "Version": "1.52.0",
  "Date": "2024-04-23",
  "Author": "Christoph Bartenhagen",
  "Maintainer": "Christoph Bartenhagen <c.bartenhagen@uni-koeln.de>",
  "Description": "RSVSim is a package for the simulation of deletions,\ninsertions, inversion, tandem-duplications and translocations\nof various sizes in any genome available as FASTA-file or\nBSgenome data package. SV breakpoints can be placed uniformly\naccross the whole genome, with a bias towards repeat regions\nand regions of high homology (for hg19) or at user-supplied\ncoordinates.",
  "License": "LGPL-3",
  "biocViews": "Sequencing",
  "Config/pak/sysreqs": "libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:10 UTC",
  "RemoteUrl": "https://github.com/bioc/RSVSim",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "44b6005952fe3284031c1c4219e7daddcea6b114",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-18 07:15:44 UTC",
    "User": "root"
  },
  "MD5sum": "b22003eaf04e65119ee591ae9090cbeb",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "RSVSim_1.52.0.tar.gz",
  "_fileid": "fa0f62fab7f973f305f92c50678c3684439fee79029b6795bae4f5cda2d880aa",
  "_filesize": 641842,
  "_sha256": "fa0f62fab7f973f305f92c50678c3684439fee79029b6795bae4f5cda2d880aa",
  "_created": "2026-06-18T07:15:44.000Z",
  "_published": "2026-06-18T07:38:26.456Z",
  "_jobs": [
    {
      "job": 82075258447,
      "time": 256,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7716665546"
    },
    {
      "job": 82075258499,
      "time": 393,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7716706932"
    },
    {
      "job": 82075258465,
      "time": 420,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7716714569"
    },
    {
      "job": 82075258444,
      "time": 219,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7716958700"
    },
    {
      "job": 82075258453,
      "time": 327,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7716995026"
    },
    {
      "job": 82074354974,
      "time": 355,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7716586404"
    },
    {
      "job": 82075258413,
      "time": 210,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7716651603"
    },
    {
      "job": 82075258488,
      "time": 348,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7716694048"
    },
    {
      "job": 82075258534,
      "time": 370,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7716700889"
    },
    {
      "job": 82075258494,
      "time": 417,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7716714137"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RSVSim",
  "_commit": {
    "id": "44b6005952fe3284031c1c4219e7daddcea6b114",
    "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": 1777379830
  },
  "_maintainer": {
    "name": "Christoph Bartenhagen",
    "email": "c.bartenhagen@uni-koeln.de",
    "login": "seismicon",
    "description": "",
    "uuid": 79155204
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "ShortRead",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19.masked",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "pwalign",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.53.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.52.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 13,
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/RSVSim.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "compareSV",
    "estimateSVSizes",
    "simulateSV"
  ],
  "_datasets": [
    {
      "name": "segDups",
      "title": "Segmental duplications",
      "object": "segmentalDuplications",
      "file": "segmentalDuplications.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "weightsMechanisms",
      "title": "Weights for SV formation mechanisms",
      "object": "weightsMechanisms",
      "file": "weightsMechanisms.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "dels",
        "ins",
        "invs",
        "dups",
        "trans"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "weightsRepeats",
      "title": "Weights for repeat region bias",
      "object": "weightsRepeats",
      "file": "weightsRepeats.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "NAHR",
        "NHR",
        "TEI",
        "VNTR",
        "Other"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compareSVs",
      "title": "Compare the simulation with a set of SVs",
      "topics": [
        "compareSV",
        "compareSV,character,character-method",
        "compareSV,character,data.frame-method",
        "compareSV,data.frame,data.frame-method"
      ]
    },
    {
      "page": "estimateSVSizes",
      "title": "Draw random structural variation sizes from a beta distribution",
      "topics": [
        "estimateSVSizes",
        "estimateSVSizes,numeric,missing,ANY,ANY,character-method",
        "estimateSVSizes,numeric,missing,ANY,ANY,missing-method",
        "estimateSVSizes,numeric,numeric,ANY,ANY,missing-method"
      ]
    },
    {
      "page": "segmentalDuplications",
      "title": "Segmental duplications",
      "topics": [
        "segDups"
      ]
    },
    {
      "page": "simulateSV",
      "title": "Structural Variant Simulation",
      "topics": [
        "simulateSV",
        "simulateSV,ANY",
        "simulateSV,ANY-method"
      ]
    },
    {
      "page": "weightsMechanisms",
      "title": "Weights for SV formation mechanisms",
      "topics": [
        "weightsMechanisms"
      ]
    },
    {
      "page": "weightsRepeats",
      "title": "Weights for repeat region bias",
      "topics": [
        "weightsRepeats"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "DelayedArray",
    "deldir",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "hwriter",
    "interp",
    "IRanges",
    "jpeg",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "png",
    "pwalign",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rhtslib",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "ShortRead",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rnw",
      "filename": "vignette.pdf",
      "title": "RSVSim: an R/Bioconductor package for the simulation of structural variations",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Structural variation simulation",
        "Simulation of biases towards SV formation mechanisms and repeat regions",
        "Simulation of additional breakpoint mutations",
        "Simulation within a genome subset",
        "Comparing two sets of SVs",
        "Setting structural variation sizes",
        "Runtime",
        "Session Information"
      ],
      "created": "2013-11-01 20:28:14",
      "modified": "2015-05-03 19:54:03",
      "commits": 2
    }
  ],
  "_score": 4.414973347970818,
  "_indexed": false,
  "_nocasepkg": "rsvsim",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/RSVSim",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.52.0",
      "date": "2026-06-18T07:20:00.000Z",
      "distro": "noble",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "4e9b05cacc7a4e00b12f3508e64f91d0357f6bd564b7cdd479c99a67d403a551",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.52.0",
      "date": "2026-06-18T07:20:28.000Z",
      "distro": "noble",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "0600403c9895839174732a361ff07e966ce7ce492ff69c2e1daa1c970b1ad55e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.52.0",
      "date": "2026-06-18T07:34:35.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "e3831a1f765f9cf69d4fbd352402fc3569a932239f978b7fd9a5de048d5a0168",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.52.0",
      "date": "2026-06-18T07:35:42.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "e810a90c1e83a3b7a9afb647ca5eb502de89bf2ba85090c94d08352e4cd7dd21",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.52.0",
      "date": "2026-06-18T07:19:51.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "563ccd174291d639271bdf75cc0a40efe2a0cda2549f88093b8ae23b2f643c72",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.52.0",
      "date": "2026-06-18T07:19:27.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "2a87274af9424b8c14b64ac68626330cd2c12a12640ed8d5aa9fdbce0390d052",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.52.0",
      "date": "2026-06-18T07:19:35.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "5daee792ad036c8caea1f296814b5d5291a8b792d71d7754933a50775e6e5c6b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.52.0",
      "date": "2026-06-18T07:20:32.000Z",
      "commit": "44b6005952fe3284031c1c4219e7daddcea6b114",
      "fileid": "b9ac97cb643d756416efd8ae1061755bdfcf4d9d1c8d608ddcbc405a94cc4d88",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742953488"
    }
  ]
}