{
  "_id": "6a227176cd65a98ecbd491c0",
  "Package": "txdbmaker",
  "Title": "Tools for making TxDb objects from genomic annotations",
  "Description": "A set of tools for making TxDb objects from genomic\nannotations from various sources (e.g. UCSC, Ensembl, and GFF\nfiles). These tools allow the user to download the genomic\nlocations of transcripts, exons, and CDS, for a given assembly,\nand to import them in a TxDb object. TxDb objects are\nimplemented in the GenomicFeatures package, together with\nflexible methods for extracting the desired features in\nconvenient formats.",
  "biocViews": "Infrastructure, DataImport, Annotation, GenomeAnnotation,\nGenomeAssembly, Genetics, Sequencing",
  "URL": "https://bioconductor.org/packages/txdbmaker",
  "BugReports": "https://github.com/Bioconductor/txdbmaker/issues",
  "Version": "1.9.0",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"H.\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"M.\", \"Carlson\", role=\"aut\"),\nperson(\"P.\", \"Aboyoun\", role=\"aut\"),\nperson(\"S.\", \"Falcon\", role=\"aut\"),\nperson(\"M.\", \"Morgan\", role=\"aut\"),\nperson(\"R.\", \"Castelo\", role=\"ctb\"),\nperson(\"M.\", \"Lawrence\", role=\"ctb\"),\nperson(\"I-Hsuan\", \"Lin\", role=\"ctb\"),\nperson(\"J.\", \"MacDonald\", role=\"ctb\"),\nperson(\"M.\", \"Ramos\", role=\"ctb\"),\nperson(\"S.\", \"Saini\", role=\"ctb\"),\nperson(\"L.\", \"Shepherd\", role=\"ctb\"))",
  "VignetteBuilder": "knitr",
  "Collate": "utils.R Ensembl-utils.R findCompatibleMarts.R TxDb-schema.R\nTxDb-CREATE-TABLE-helpers.R makeTxDb.R makeTxDbFromUCSC.R\nmakeTxDbFromBiomart.R makeTxDbFromEnsembl.R\nmakeTxDbFromGRanges.R makeTxDbFromGFF.R makeFeatureDbFromUCSC.R\nmakeTxDbPackage.R zzz.R",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:30 UTC",
  "RemoteUrl": "https://github.com/bioc/txdbmaker",
  "RemoteRef": "HEAD",
  "RemoteSha": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-05 06:33:21 UTC",
    "User": "root"
  },
  "Author": "H. Pagès [aut, cre],\nM. Carlson [aut],\nP. Aboyoun [aut],\nS. Falcon [aut],\nM. Morgan [aut],\nR. Castelo [ctb],\nM. Lawrence [ctb],\nI-Hsuan Lin [ctb],\nJ. MacDonald [ctb],\nM. Ramos [ctb],\nS. Saini [ctb],\nL. Shepherd [ctb]",
  "Maintainer": "H. Pagès <hpages.on.github@gmail.com>",
  "MD5sum": "e0a0b2caeac95ed89879931ec78ee3a5",
  "_user": "bioc",
  "_type": "src",
  "_file": "txdbmaker_1.9.0.tar.gz",
  "_fileid": "8888b3e1aa81d128d60ab87c5c83c4c84bfe70466bb7e7396e5fd33c55604b94",
  "_filesize": 992599,
  "_sha256": "8888b3e1aa81d128d60ab87c5c83c4c84bfe70466bb7e7396e5fd33c55604b94",
  "_created": "2026-06-05T06:33:21.000Z",
  "_published": "2026-06-05T06:49:26.115Z",
  "_jobs": [
    {
      "job": 79676675006,
      "time": 188,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7430358122"
    },
    {
      "job": 79676675025,
      "time": 890,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7430525319"
    },
    {
      "job": 79676675055,
      "time": 876,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7430522241"
    },
    {
      "job": 79676675063,
      "time": 778,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7430499646"
    },
    {
      "job": 79676675041,
      "time": 402,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7430410508"
    },
    {
      "job": 79676031494,
      "time": 319,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7430311153"
    },
    {
      "job": 79676675043,
      "time": 162,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7430351048"
    },
    {
      "job": 79676675067,
      "time": 862,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7430519150"
    },
    {
      "job": 79676675049,
      "time": 873,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7430521655"
    },
    {
      "job": 79676675062,
      "time": 809,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7430506988"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/txdbmaker",
  "_commit": {
    "id": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
    "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": 1777381350
  },
  "_maintainer": {
    "name": "H. Pagès",
    "email": "hpages.on.github@gmail.com",
    "login": "hpages",
    "linkedin": "in/hervé-pagès-5038527",
    "description": "",
    "uuid": 8810451
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.47.6",
      "role": "Depends"
    },
    {
      "package": "Seqinfo",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Depends"
    },
    {
      "package": "GenomicFeatures",
      "version": ">= 1.61.4",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "rjson",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "RSQLite",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "UCSC.utils",
      "version": ">= 1.7.1",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "BiocIO",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "version": ">= 2.59.1",
      "role": "Imports"
    },
    {
      "package": "RMariaDB",
      "role": "Suggests"
    },
    {
      "package": "ensembldb",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDbData",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 63,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-26",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 4
    },
    {
      "week": "2025-48",
      "n": 2
    },
    {
      "week": "2025-50",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 3
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "dataimport",
    "annotation",
    "genomeannotation",
    "genomeassembly",
    "genetics",
    "sequencing",
    "bioconductor-package",
    "core-package"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "hpages",
      "count": 40,
      "uuid": 8810451
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "ycl6",
      "count": 1,
      "uuid": 9032946
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    },
    {
      "user": "rcastelo",
      "count": 1,
      "uuid": 1677433
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 7733,
    "source": "https://www.bioconductor.org/packages/stats/bioc/txdbmaker"
  },
  "_devurl": "https://github.com/bioconductor/txdbmaker",
  "_searchresults": 305,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/txdbmaker.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioconductor/txdbmaker",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "browseUCSCtrack",
    "getChromInfoFromBiomart",
    "makeFDbPackageFromUCSC",
    "makeFeatureDbFromUCSC",
    "makePackageName",
    "makeTxDb",
    "makeTxDbFromBiomart",
    "makeTxDbFromEnsembl",
    "makeTxDbFromGFF",
    "makeTxDbFromGRanges",
    "makeTxDbFromUCSC",
    "makeTxDbPackage",
    "makeTxDbPackageFromBiomart",
    "makeTxDbPackageFromUCSC",
    "supportedUCSCFeatureDbTables",
    "supportedUCSCFeatureDbTracks",
    "supportedUCSCtables",
    "UCSCFeatureDbTableSchema"
  ],
  "_help": [
    {
      "page": "txdbmaker-package",
      "title": "Tools for making TxDb objects from genomic annotations",
      "topics": [
        "txdbmaker-package",
        "txdbmaker"
      ]
    },
    {
      "page": "makeFeatureDbFromUCSC",
      "title": "Making a FeatureDb object from annotations available at the UCSC Genome Browser",
      "topics": [
        "makeFeatureDbFromUCSC",
        "supportedUCSCFeatureDbTables",
        "supportedUCSCFeatureDbTracks",
        "UCSCFeatureDbTableSchema"
      ]
    },
    {
      "page": "makeTxDb",
      "title": "Making a TxDb object from user supplied annotations",
      "topics": [
        "makeTxDb"
      ]
    },
    {
      "page": "makeTxDbFromBiomart",
      "title": "Make a TxDb object from annotations available on a BioMart database",
      "topics": [
        "getChromInfoFromBiomart",
        "makeTxDbFromBiomart"
      ]
    },
    {
      "page": "makeTxDbFromEnsembl",
      "title": "Make a TxDb object from an Ensembl database",
      "topics": [
        "makeTxDbFromEnsembl"
      ]
    },
    {
      "page": "makeTxDbFromGFF",
      "title": "Make a TxDb object from annotations available as a GFF3 or GTF file",
      "topics": [
        "makeTxDbFromGFF"
      ]
    },
    {
      "page": "makeTxDbFromGRanges",
      "title": "Make a TxDb object from a GRanges object",
      "topics": [
        "makeTxDbFromGRanges"
      ]
    },
    {
      "page": "makeTxDbFromUCSC",
      "title": "Make a TxDb object from annotations available at the UCSC Genome Browser",
      "topics": [
        "browseUCSCtrack",
        "makeTxDbFromUCSC",
        "supportedUCSCtables"
      ]
    },
    {
      "page": "makeTxDbPackage",
      "title": "Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.",
      "topics": [
        "makeFDbPackageFromUCSC",
        "makePackageName",
        "makeTxDbPackage",
        "makeTxDbPackageFromBiomart",
        "makeTxDbPackageFromUCSC"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/txdbmaker/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "txdbmaker.Rmd",
      "filename": "txdbmaker.html",
      "title": "Making TxDb Objects",
      "author": "Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing the txdbmaker package",
        "Using makeTxDbFromUCSC",
        "Using makeTxDbFromBiomart",
        "Using makeTxDbFromEnsembl",
        "Using makeTxDbFromGFF",
        "Saving and Loading a TxDb Object",
        "Using makeTxDbPackageFromUCSC and makeTxDbPackageFromBiomart",
        "Session Information"
      ],
      "created": "2023-10-28 08:22:26",
      "modified": "2024-04-04 17:26:59",
      "commits": 3
    }
  ],
  "_score": 10.494207693712337,
  "_indexed": true,
  "_nocasepkg": "txdbmaker",
  "_universes": [
    "bioc",
    "hpages",
    "bioconductor"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-06-05T06:37:29.000Z",
      "distro": "noble",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "58274da7f932ce8a7a4e83c1ca4906fff7ab13d965861ff607698ed01ce74738",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-06-05T06:36:41.000Z",
      "distro": "noble",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "b3aaa4318de11ba58271958f9fb83b7644117d6e5eac9759a7c6328c16f2a4b9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-06-05T06:35:36.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "f8c6aa91cfab7e134d97870126eed4aad30ef8b1a950271b2cdacbcdb417f6c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-06-05T06:35:33.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "c897ed581c0d5bfc3f815379b221d5ead270aee7a546a5a7ba3ce05b99b7bd3f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-06-05T06:36:48.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "5be2dd3c20ed7ea7554e54f3e28fb2bc8bd66fb75453622192fc426444a080a5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-06-05T06:35:52.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "82b0f0fad77d16d22d0f09ea95cce3346ac9d81d0bbb55b6cace801a3f6b3f00",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-06-05T06:36:03.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "968e8681cab911d9e9a85e7a7a15b5e48221583fe9b1da14d161bc19a9ba2c2a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-06-05T06:35:36.000Z",
      "commit": "d57df0dab413fbc9b403b871c5c6fc6e919a37b6",
      "fileid": "1dbf345f64be205245b5ea2a12dc4dbe58c0c53d291f094f79e5907dc8a3383f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26999347967"
    }
  ]
}