{
  "_id": "6a4943c618cdde069385ed9c",
  "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": "2026-07-04 13:30:16 UTC",
    "User": "root"
  },
  "Author": "Alex Pickering [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-0002-6759>)",
  "Maintainer": "Alex Pickering <alexvpickering@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GEOfastq_1.21.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/95596e07f69c618a49ca433d71f7691beaaa251b990085868755f3fa46e3488d",
  "_filesize": 101587,
  "_sha256": "95596e07f69c618a49ca433d71f7691beaaa251b990085868755f3fa46e3488d",
  "_expires": "2026-10-12T17:32:52.000Z",
  "_created": "2026-07-04T13:30:16.000Z",
  "_published": "2026-07-04T17:32:54.192Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395",
  "_status": "success",
  "_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": "resolute",
  "_jobs": [
    {
      "job": 85152543341,
      "time": 176,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8082144578"
    },
    {
      "job": 85152543358,
      "time": 321,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8082163169"
    },
    {
      "job": 85152543413,
      "time": 227,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082150908"
    },
    {
      "job": 85152543347,
      "time": 94,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8082134353"
    },
    {
      "job": 85152543330,
      "time": 108,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082136351"
    },
    {
      "job": 85152543197,
      "time": 281,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082122264"
    },
    {
      "job": 85152543403,
      "time": 177,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8082144845"
    },
    {
      "job": 85152543273,
      "time": 110,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8082136567"
    },
    {
      "job": 85152543350,
      "time": 89,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8082133824"
    },
    {
      "job": 85152543412,
      "time": 103,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8082135672"
    }
  ],
  "_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",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/alexvpickering/geofastq",
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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": "2026-07-04T13:34:30.000Z",
      "distro": "resolute",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/6301489aaba353a06ed02967154b9f9046a4ac983af67e998bd483408f85c3b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-07-04T13:33:50.000Z",
      "distro": "resolute",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/4f68b21c4807aa026f71fce4cae7e156380d5b781a8d6d2c17e95b70ddf568e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-07-04T13:31:37.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/94813ac38cbb437f4eff779c04d5da522de2a66c99d3c001acafe87673885822",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-07-04T13:31:49.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/49516cb67f65a0f603cdd7ce567cd4d5a3152125933a541c8345385a72e82f10",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.0",
      "date": "2026-07-04T13:33:29.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/bbd98a17c375941530f823fd1145b29e6e361b7ad8739427747e23dbb3b70c6d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-07-04T13:32:00.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/ac2cf1cff6ddf136b45d4b5c5b86d2e93c19706690a3ef33b6e10f49167ff794",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-07-04T13:31:38.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/54e37a531998091fc48aa9b54276f10b17d7089cacac052518bd56e8767d9b7c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-07-04T13:31:48.000Z",
      "commit": "b16140106c9441ca126dbc49f92489589df04a94",
      "fileid": "https://r2.ropensci.org/4bc384b53c51fea90932ac7a8fe22a9411928da6f9a6758858bf117c2b892d0a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707638395"
    }
  ]
}