{
  "_id": "6a26a2ad24555f66ed52241e",
  "Package": "BSgenomeForge",
  "Title": "Forge your own BSgenome data package",
  "Description": "A set of tools to forge BSgenome data packages. Supersedes\nthe old seed-based tools from the BSgenome software package.\nThis package allows the user to create a BSgenome data package\nin one function call, simplifying the old seed-based process.",
  "biocViews": "Infrastructure, DataRepresentation, GenomeAssembly,\nAnnotation, GenomeAnnotation, Sequencing, Alignment,\nDataImport, SequenceMatching",
  "URL": "https://bioconductor.org/packages/BSgenomeForge",
  "BugReports": "https://github.com/Bioconductor/BSgenomeForge/issues",
  "Version": "1.12.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"Atuhurira Kirabo\", \"Kakopo\", role=\"aut\"),\nperson(\"Emmanuel Chigozie\", \"Elendu\", role=\"ctb\"),\nperson(\"Prisca Chidimma\", \"Maduka\", role=\"ctb\"))",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:26 UTC",
  "RemoteUrl": "https://github.com/bioc/BSgenomeForge",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 10:59:34 UTC",
    "User": "root"
  },
  "Author": "Hervé Pagès [aut, cre],\nAtuhurira Kirabo Kakopo [aut],\nEmmanuel Chigozie Elendu [ctb],\nPrisca Chidimma Maduka [ctb]",
  "Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
  "MD5sum": "f608bb828b06f623a7a7acfe35ac74b5",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "BSgenomeForge_1.12.0.tar.gz",
  "_fileid": "9550a2daf8b67142e5185be40fb9dd3ddb272170d984885c1bfda9e0e778d309",
  "_filesize": 385895,
  "_sha256": "9550a2daf8b67142e5185be40fb9dd3ddb272170d984885c1bfda9e0e778d309",
  "_created": "2026-06-08T10:59:34.000Z",
  "_published": "2026-06-08T11:08:29.058Z",
  "_jobs": [
    {
      "job": 80078850713,
      "time": 280,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7478399969"
    },
    {
      "job": 80078850854,
      "time": 470,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7478464442"
    },
    {
      "job": 80078850798,
      "time": 459,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7478460687"
    },
    {
      "job": 80078850775,
      "time": 217,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7478380670"
    },
    {
      "job": 80078850726,
      "time": 242,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7478388251"
    },
    {
      "job": 80077913556,
      "time": 337,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478307433"
    },
    {
      "job": 80078850758,
      "time": 201,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478374585"
    },
    {
      "job": 80078850940,
      "time": 329,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7478417732"
    },
    {
      "job": 80078850877,
      "time": 308,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7478411237"
    },
    {
      "job": 80078850841,
      "time": 302,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7478407685"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 4,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BSgenomeForge",
  "_commit": {
    "id": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
    "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": 1777381226
  },
  "_maintainer": {
    "name": "Hervé Pagès",
    "email": "hpages.on.github@gmail.com",
    "login": "hpages",
    "linkedin": "in/hervé-pagès-5038527",
    "description": "",
    "uuid": 8810451
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "Seqinfo",
      "role": "Depends"
    },
    {
      "package": "GenomeInfoDb",
      "version": ">= 1.45.5",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.77.2",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "version": ">= 1.77.1",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.47.6",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Imports"
    },
    {
      "package": "BiocIO",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "version": ">= 1.69.1",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "Rsamtools",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Celegans.UCSC.ce2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 3
    },
    {
      "week": "2025-48",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.13.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.12.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "datarepresentation",
    "genomeassembly",
    "annotation",
    "genomeannotation",
    "sequencing",
    "alignment",
    "dataimport",
    "sequencematching",
    "bioconductor-package",
    "core-package"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "hpages",
      "count": 71,
      "uuid": 8810451
    },
    {
      "user": "kakopo",
      "count": 15,
      "uuid": 52150109
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "jeroen",
      "count": 1,
      "uuid": 216319
    },
    {
      "user": "priceless-p",
      "count": 1,
      "uuid": 88077456
    },
    {
      "user": "simplecodez",
      "count": 1,
      "uuid": 102396467
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 458,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BSgenomeForge"
  },
  "_devurl": "https://github.com/bioconductor/bsgenomeforge",
  "_searchresults": 23,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BSgenomeForge.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/bioconductor/bsgenomeforge",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "downloadGenomicSequencesFromNCBI",
    "downloadGenomicSequencesFromUCSC",
    "fastaTo2bit",
    "forgeBSgenomeDataPkg",
    "forgeBSgenomeDataPkgFromNCBI",
    "forgeBSgenomeDataPkgFromTwobitFile",
    "forgeBSgenomeDataPkgFromUCSC",
    "forgeMaskedBSgenomeDataPkg",
    "forgeMasksFiles",
    "forgeSeqFiles",
    "forgeSeqlengthsRdaFile",
    "forgeSeqlengthsRdsFile"
  ],
  "_help": [
    {
      "page": "BSgenomeForge-package",
      "title": "The BSgenomeForge package",
      "topics": [
        "BSgenomeForge-package",
        "BSgenomeForge"
      ]
    },
    {
      "page": "AdvancedBSgenomeForge",
      "title": "Advanced BSgenomeForge functions",
      "topics": [
        "AdvancedBSgenomeForge",
        "BSgenomeDataPkgSeed",
        "BSgenomeDataPkgSeed-class",
        "class:BSgenomeDataPkgSeed",
        "forgeBSgenomeDataPkg",
        "forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method",
        "forgeBSgenomeDataPkg,character-method",
        "forgeBSgenomeDataPkg,list-method",
        "forgeMaskedBSgenomeDataPkg",
        "forgeMaskedBSgenomeDataPkg,character-method",
        "forgeMaskedBSgenomeDataPkg,list-method",
        "forgeMaskedBSgenomeDataPkg,MaskedBSgenomeDataPkgSeed-method",
        "forgeMasksFiles",
        "forgeSeqFiles",
        "forgeSeqlengthsRdaFile",
        "forgeSeqlengthsRdsFile"
      ]
    },
    {
      "page": "downloadGenomicSequencesFromNCBI",
      "title": "Download genomic sequences from NCBI",
      "topics": [
        "downloadGenomicSequencesFromNCBI"
      ]
    },
    {
      "page": "downloadGenomicSequencesFromUCSC",
      "title": "Download genomic sequences from UCSC",
      "topics": [
        "downloadGenomicSequencesFromUCSC"
      ]
    },
    {
      "page": "fastaTo2bit",
      "title": "Convert files from FASTA to 2bit",
      "topics": [
        "fastaTo2bit"
      ]
    },
    {
      "page": "forgeBSgenomeDataPkgFromNCBI",
      "title": "Create a BSgenome data package from an NCBI assembly",
      "topics": [
        "forgeBSgenomeDataPkgFromNCBI"
      ]
    },
    {
      "page": "forgeBSgenomeDataPkgFromTwobitFile",
      "title": "Create a BSgenome data package from a 2bit file",
      "topics": [
        "forgeBSgenomeDataPkgFromTwobitFile"
      ]
    },
    {
      "page": "forgeBSgenomeDataPkgFromUCSC",
      "title": "Create a BSgenome data package from a UCSC genome",
      "topics": [
        "forgeBSgenomeDataPkgFromUCSC"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/BSgenomeForge/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "BSgenome",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DelayedArray",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "UCSC.utils",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "QuickBSgenomeForge.Rmd",
      "filename": "QuickBSgenomeForge.html",
      "title": "A quick introduction to the BSgenomeForge package",
      "author": "Atuhurira Kirabo Kakopo, Hervé Pagès",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Basic usage",
        "Using forgeBSgenomeDataPkgFromNCBI()",
        "Using forgeBSgenomeDataPkgFromUCSC()",
        "Final steps",
        "sessionInfo()"
      ],
      "created": "2024-03-31 00:57:47",
      "modified": "2024-04-08 21:07:56",
      "commits": 2
    },
    {
      "source": "AdvancedBSgenomeForge.Rnw",
      "filename": "AdvancedBSgenomeForge.pdf",
      "title": "Advanced BSgenomeForge usage",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "How to forge a BSgenome data package with bare sequences",
        "How to forge a BSgenome data package with masked sequences",
        "Session information"
      ],
      "created": "2024-03-31 00:57:47",
      "modified": "2024-03-31 00:57:47",
      "commits": 1
    }
  ],
  "_score": 6.6047658847038875,
  "_indexed": false,
  "_nocasepkg": "bsgenomeforge",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/BSgenomeForge",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.12.0",
      "date": "2026-06-08T11:04:51.000Z",
      "distro": "noble",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "032490481609ea7ec1122eb08ec818d09e1ca38802da29f46b163cbc0bcbb122",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.12.0",
      "date": "2026-06-08T11:05:00.000Z",
      "distro": "noble",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "98e5f8d0eedd449f1fd6e6e556234cae99005b5aecbf0e1d345a64278b9efdc7",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.12.0",
      "date": "2026-06-08T11:01:57.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "11cd12eeca251f001005ed4e658014bf017553a65b6c66618aa733fbe8323089",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.12.0",
      "date": "2026-06-08T11:01:56.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "8e67b5a783a303133eba6874f65edf4929b29cc16a7896f88e891870b464df99",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.12.0",
      "date": "2026-06-08T11:03:33.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "0ed75c64692f21a6ce32716f05abe8e1fafd8f070de2321366967163abde27da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.12.0",
      "date": "2026-06-08T11:02:13.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "e1a66aca2fbf79ec6128f784f001e060a763fa0a4748711deacaebed285db0e2",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.12.0",
      "date": "2026-06-08T11:02:31.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "96f0a430ac66283607ea7ef10e8b10f8a6bea3b9bb365a265cca42fb329447e2",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.12.0",
      "date": "2026-06-08T11:01:56.000Z",
      "commit": "d920cea8b5fd8fa23bf8807d308c2788751281e4",
      "fileid": "94bcf9cb826633e5525594f121ecebb15a553727f52878551658538c6f69b747",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27132841743"
    }
  ]
}