{
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  "Package": "ExpressionAtlas",
  "Version": "2.5.0",
  "Date": "2025/09/01",
  "Title": "Download datasets from EMBL-EBI Expression Atlas",
  "Authors@R": "c(person(given = \"Maria\",\nfamily = \"Keays\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2034-601X\")\n),\nperson(given = \"Pedro\",\nfamily = \"Madrigal\",\nrole = c(\"aut\"),\nemail = \"pmadrigal@ebi.ac.uk\",\ncomment = c(ORCID = \"0000-0003-1959-8199\")\n),\nperson(given = \"Anil\",\nfamily = \"Thanki\",\nrole = c(\"cre\"),\nemail = \"anilthanki@ebi.ac.uk\",\ncomment = c(ORCID = \"0000-0002-8941-444X\")\n)\n)",
  "Description": "This package is for searching for datasets in EMBL-EBI\nExpression Atlas, and downloading them into R for further\nanalysis. Each Expression Atlas dataset is represented as a\nSimpleList object with one element per platform. Sequencing\ndata is contained in a SummarizedExperiment object, while\nmicroarray data is contained in an ExpressionSet or MAList\nobject.",
  "biocViews": "ExpressionData, ExperimentData, SequencingData,\nMicroarrayData, ArrayExpress",
  "VignetteBuilder": "knitr",
  "Collate": "functions.R",
  "License": "GPL (>= 3)",
  "LazyLoad": "yes",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "cmake make libuv1-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:41 UTC",
  "RemoteUrl": "https://github.com/bioc/ExpressionAtlas",
  "RemoteRef": "HEAD",
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  "Packaged": {
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    "User": "root"
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  "Author": "Maria Keays [aut] (ORCID: <https://orcid.org/0000-0003-2034-601X>),\nPedro Madrigal [aut] (ORCID: <https://orcid.org/0000-0003-1959-8199>),\nAnil Thanki [cre] (ORCID: <https://orcid.org/0000-0002-8941-444X>)",
  "Maintainer": "Anil Thanki <anilthanki@ebi.ac.uk>",
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  "_created": "2026-07-04T00:46:40.000Z",
  "_published": "2026-07-04T17:03:29.109Z",
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 13
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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 odd y following creation of RELEASE_3_23 branch\n",
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    "name": "Anil Thanki",
    "email": "anilthanki@ebi.ac.uk",
    "login": "anilthanki",
    "mastodon": "@anilthanki@mastodon.social",
    "bluesky": "@anilthanki.bsky.social",
    "linkedin": "in/anilthanki",
    "twitter": "@anilthanki",
    "description": "",
    "uuid": 3940626,
    "orcid": "0000-0002-8941-444X"
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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    },
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    "experimentdata",
    "sequencingdata",
    "microarraydata",
    "arrayexpress"
  ],
  "_userbio": {
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    "type": "organization",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_searchresults": 24,
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "getAtlasData",
    "getAtlasExperiment",
    "searchAtlasExperiments"
  ],
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      "name": "allExps",
      "title": "A SimpleList containing some dummy Expression Atlas datasets",
      "object": "allExps",
      "file": "allExps.rda",
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      "page": "allExps",
      "title": "A SimpleList containing some dummy Expression Atlas datasets",
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      ]
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      "page": "atlasRes",
      "title": "A DataFrame listing some Expression Atlas experiments",
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    {
      "page": "getAtlasData",
      "title": "Download data from multiple Expression Atlas experiments",
      "topics": [
        "getAtlasData"
      ]
    },
    {
      "page": "getAtlasExperiment",
      "title": "Download data for an Expression Atlas experiment",
      "topics": [
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      ]
    },
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      "title": "A SimpleList containing a dummy RNA-seq Expression Atlas dataset",
      "topics": [
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    {
      "page": "searchAtlasExperiments",
      "title": "Search for Expression Atlas experiments",
      "topics": [
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      ]
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        "Searching and downloading Expression Atlas data",
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        "Downloading a single Expression Atlas experiment summary"
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      "created": "2016-02-22 18:03:39",
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