{
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  "Type": "Package",
  "Title": "Downloads ENA Fastqs With GEO Accessions",
  "Version": "1.20.0",
  "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-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:38 UTC",
  "RemoteUrl": "https://github.com/bioc/GEOfastq",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a168ade6fb68e8b81eb311ae98057ac97674da15",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 07:03:16 UTC",
    "User": "root"
  },
  "Author": "Alex Pickering [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-0002-6759>)",
  "Maintainer": "Alex Pickering <alexvpickering@gmail.com>",
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    "note": 7
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    "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",
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  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-44",
      "n": 2
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    "rnaseq",
    "dataimport",
    "bioinformatics",
    "fastq",
    "gene-expression",
    "geo",
    "rna-seq"
  ],
  "_stars": 4,
  "_contributors": [
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/GEOfastq"
  },
  "_devurl": "https://github.com/alexvpickering/geofastq",
  "_searchresults": 12,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "manual.pdf"
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  "_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/RELEASE_3_23/README.md",
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      "source": "GEOfastq.Rmd",
      "filename": "GEOfastq.html",
      "title": "Using the GEOfastq Package",
      "engine": "knitr::rmarkdown",
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        "Overview of GEOfastq",
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      "created": "2020-10-26 21:59:32",
      "modified": "2020-11-25 18:30:22",
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