{
  "_id": "6a1acee91d7bb097a09e0218",
  "Package": "GEOfastq",
  "Type": "Package",
  "Title": "Downloads ENA Fastqs With GEO Accessions",
  "Version": "1.21.0",
  "Authors@R": "person(\"Alex\", \"Pickering\", email=\"alexvpickering@gmail.com\", \nrole=c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-0002-6759\"))",
  "Description": "GEOfastq is used to download fastq files from the European\nNucleotide Archive (ENA) starting with an accession from the\nGene Expression Omnibus (GEO). To do this, sample metadata is\nretrieved from GEO and the Sequence Read Archive (SRA). SRA run\naccessions are then used to construct FTP and aspera download\nlinks for fastq files generated by the ENA.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "BugReports": "https://github.com/alexvpickering/GEOfastq/issues",
  "biocViews": "RNASeq, DataImport",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libicu-dev libxml2-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:38 UTC",
  "RemoteUrl": "https://github.com/bioc/GEOfastq",
  "RemoteRef": "HEAD",
  "RemoteSha": "b16140106c9441ca126dbc49f92489589df04a94",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:15:21 UTC",
    "User": "root"
  },
  "Author": "Alex Pickering [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-0002-6759>)",
  "Maintainer": "Alex Pickering <alexvpickering@gmail.com>",
  "MD5sum": "36cb3bc7fc432a2416a8cca3117dd7c6",
  "_user": "bioc",
  "_type": "src",
  "_file": "GEOfastq_1.21.0.tar.gz",
  "_fileid": "a15663ab784df4a1f760bddaa648edc6dcb8ff5947e286b515a24f348f36acf4",
  "_filesize": 99344,
  "_sha256": "a15663ab784df4a1f760bddaa648edc6dcb8ff5947e286b515a24f348f36acf4",
  "_created": "2026-05-30T08:15:21.000Z",
  "_published": "2026-05-30T11:50:01.380Z",
  "_jobs": [
    {
      "job": 78635936290,
      "time": 146,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306767490"
    },
    {
      "job": 78635936282,
      "time": 247,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306776592"
    },
    {
      "job": 78635936279,
      "time": 180,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306770598"
    },
    {
      "job": 78635936278,
      "time": 163,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307959581"
    },
    {
      "job": 78635936271,
      "time": 188,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307961570"
    },
    {
      "job": 78635697040,
      "time": 279,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306753195"
    },
    {
      "job": 78635936270,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306765519"
    },
    {
      "job": 78635936300,
      "time": 108,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7306763926"
    },
    {
      "job": 78635936288,
      "time": 114,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7306764340"
    },
    {
      "job": 78635936296,
      "time": 100,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306762996"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GEOfastq",
  "_commit": {
    "id": "b16140106c9441ca126dbc49f92489589df04a94",
    "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": 1777380878
  },
  "_maintainer": {
    "name": "Alex Pickering",
    "email": "alexvpickering@gmail.com",
    "login": "alexvpickering",
    "description": "",
    "uuid": 15719520,
    "orcid": "0000-0002-0002-6759"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "rvest",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "BiocCheck",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "rnaseq",
    "dataimport",
    "bioinformatics",
    "fastq",
    "gene-expression",
    "geo",
    "rna-seq"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "alexvpickering",
      "count": 49,
      "uuid": 15719520
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 346,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GEOfastq"
  },
  "_devurl": "https://github.com/alexvpickering/geofastq",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GEOfastq.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/alexvpickering/geofastq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "crawl_gse",
    "crawl_gsms",
    "extract_gsms",
    "get_dldir",
    "get_fastqs"
  ],
  "_help": [
    {
      "page": "crawl_gse",
      "title": "Get GSE text from GEO",
      "topics": [
        "crawl_gse"
      ]
    },
    {
      "page": "crawl_gsms",
      "title": "Crawls SRX pages for each GSM to get metadata.",
      "topics": [
        "crawl_gsms"
      ]
    },
    {
      "page": "extract_gsms",
      "title": "Extract GSMs needed to download RNA-seq data for a series",
      "topics": [
        "extract_gsms"
      ]
    },
    {
      "page": "get_dldir",
      "title": "Gets part of path to download bulk RNAseq sample from EBI or NCBI",
      "topics": [
        "get_dldir"
      ]
    },
    {
      "page": "get_fastqs",
      "title": "Download and RNA-seq fastq data from EBI",
      "topics": [
        "get_fastqs"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GEOfastq/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "bitops",
    "cli",
    "codetools",
    "curl",
    "doParallel",
    "foreach",
    "glue",
    "httr",
    "iterators",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "R6",
    "Rcpp",
    "RCurl",
    "rlang",
    "rvest",
    "selectr",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "utf8",
    "vctrs",
    "xml2"
  ],
  "_vignettes": [
    {
      "source": "GEOfastq.Rmd",
      "filename": "GEOfastq.html",
      "title": "Using the GEOfastq Package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Overview of GEOfastq",
        "Getting Started using GEOfastq",
        "Session info"
      ],
      "created": "2020-10-26 21:59:32",
      "modified": "2020-11-25 18:30:22",
      "commits": 3
    }
  ],
  "_score": 4.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "geofastq",
  "_universes": [
    "bioc",
    "alexvpickering"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T08:19:07.000Z",
      "distro": "noble",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "277c86678d04ff68cac3ee946a0eb7862691fe6cfd35a125c7e223ca3b253e9a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T08:18:12.000Z",
      "distro": "noble",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "999ba55800379c4cf3a077bdb9791228cfa7bc36e8a36356a6cee2ff7dba5f9b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T11:48:43.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "8500bc96d4f4e6d5c91d2331e5e04fd475db6013d7c7cc684b0ff2d203cf639e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T11:48:07.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "9f5102b20f5c602e0ebab4dbf39dcf2b39c133aaafa35413e89bf8c7a9991d49",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.0",
      "date": "2026-05-30T08:17:47.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "83177bc556351c6b04a270a042a6bab03d1f0f43d3636ca929ca44cf411711a8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:17:04.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "1e85c0dd7606137dadaf31c713cbbc619f5c62b111a1733866558cd1b63bd6a8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:17:06.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "7277c40ca8855097b64af560872bce7df3894851830cfb6278fd501fe9326512",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:16:52.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "846c87caa96b95eb457adb9c1471be27f564d32e3943ac2c650b3d4e69f634d9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678900018"
    }
  ]
}