{
  "_id": "6a19ed931d7bb097a09c8203",
  "Package": "GwasDataImport",
  "Title": "Import EBI Data to OpenGWAS",
  "Version": "0.2.1",
  "Authors@R": "c(\nperson(\"Gibran\", \"Hemani\", , \"g.hemani@bristol.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0920-1055\")),\nperson(\"Philip\", \"Haycock\", , \"philip.haycock@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5001-3350\")),\nperson(\"Tom\", \"Palmer\", , \"tom.palmer@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4655-4511\"))\n)",
  "URL": "https://mrcieu.github.io/GwasDataImport",
  "Description": "Determine the new EBI data not present in OpenGWAS.\nDownload dataset and import metadata. Upload processed data and\nmetadata to OpenGWAS.",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "Remotes": [
    "github::MRCIEU/CheckSumStats",
    "github::MRCIEU/gwasvcf",
    "github::mrcieu/ieugwasr"
  ],
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2026-02-17 12:22:21 UTC",
  "RemoteUrl": "https://github.com/MRCIEU/GwasDataImport",
  "RemoteRef": "HEAD",
  "RemoteSha": "91c27f37aa116442b125fd054c3cef3ad14a8266",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 19:37:07 UTC",
    "User": "root"
  },
  "Author": "Gibran Hemani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0920-1055>),\nPhilip Haycock [aut] (ORCID: <https://orcid.org/0000-0001-5001-3350>),\nTom Palmer [aut] (ORCID: <https://orcid.org/0000-0003-4655-4511>)",
  "Maintainer": "Gibran Hemani <g.hemani@bristol.ac.uk>",
  "MD5sum": "aa8533b40e883dbd11f97f5dc198044e",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "GwasDataImport_0.2.1.tar.gz",
  "_fileid": "b021001ef75ed3da7b04fdc283d6f8d52722bd50a75baaa337217917fa3e8ffe",
  "_filesize": 18732521,
  "_sha256": "b021001ef75ed3da7b04fdc283d6f8d52722bd50a75baaa337217917fa3e8ffe",
  "_created": "2026-05-29T19:37:07.000Z",
  "_published": "2026-05-29T19:48:35.409Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78573737291,
      "time": 210,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7299527997"
    },
    {
      "job": 78573737226,
      "time": 213,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7299528630"
    },
    {
      "job": 78573737265,
      "time": 104,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7299640798"
    },
    {
      "job": 78573737282,
      "time": 115,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7299657387"
    },
    {
      "job": 78572910602,
      "time": 311,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299457632"
    },
    {
      "job": 78573737246,
      "time": 194,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299522858"
    },
    {
      "job": 78573737260,
      "time": 132,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7299503651"
    },
    {
      "job": 78573737234,
      "time": 137,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7299504606"
    },
    {
      "job": 78573737303,
      "time": 140,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7299505585"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/MRCIEU/GwasDataImport",
  "_commit": {
    "id": "91c27f37aa116442b125fd054c3cef3ad14a8266",
    "author": "JasonQiu <22163445+JasonQiu@users.noreply.github.com>",
    "committer": "JasonQiu <22163445+JasonQiu@users.noreply.github.com>",
    "message": "docs: Update website\n",
    "time": 1771330941
  },
  "_maintainer": {
    "name": "Gibran Hemani",
    "email": "g.hemani@bristol.ac.uk",
    "login": "explodecomputer",
    "description": "",
    "uuid": 1924940,
    "orcid": "0000-0003-0920-1055"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "ieugwasr",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "CheckSumStats",
      "role": "Suggests"
    },
    {
      "package": "gwasvcf",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "mrcieu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-48",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "explodecomputer",
      "count": 69,
      "uuid": 1924940
    },
    {
      "user": "remlapmot",
      "count": 61,
      "uuid": 3777473
    },
    {
      "user": "jasonqiu",
      "count": 17,
      "uuid": 22163445
    },
    {
      "user": "mightyphil2000",
      "count": 7,
      "uuid": 10760254
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GwasDataImport"
  },
  "_devurl": "https://github.com/mrcieu/gwasdataimport",
  "_pkgdown": "https://mrcieu.github.io/GwasDataImport",
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GwasDataImport.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "%>%",
    "being_processed",
    "create_build_reference",
    "create_marts",
    "Dataset",
    "determine_build",
    "determine_build_biomart",
    "determine_build_position",
    "determine_new_datasets",
    "ebi_datasets",
    "EbiDataset",
    "get_ftp_path",
    "get_positions",
    "liftover_gwas",
    "listftp"
  ],
  "_datasets": [
    {
      "name": "build_ref",
      "title": "",
      "object": "build_ref",
      "class": [
        "data.frame"
      ],
      "fields": [
        "rsid",
        "b36",
        "b37",
        "b38"
      ],
      "rows": 236061,
      "table": true,
      "tojson": true
    },
    {
      "name": "mart36",
      "title": "",
      "object": "marts",
      "class": [
        "Mart"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mart37",
      "title": "",
      "object": "marts",
      "class": [
        "Mart"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mart38",
      "title": "",
      "object": "marts",
      "class": [
        "Mart"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "being_processed",
      "title": "being_processed",
      "topics": [
        "being_processed"
      ]
    },
    {
      "page": "create_build_reference",
      "title": "Create dataset of some hm3 SNPs and their build positions",
      "topics": [
        "create_build_reference"
      ]
    },
    {
      "page": "create_marts",
      "title": "Create marts for b36-38",
      "topics": [
        "create_marts"
      ]
    },
    {
      "page": "Dataset",
      "title": "Object that downloads, develops and uploads GWAS summary datasets for IEU OpenGWAS database",
      "topics": [
        "Dataset"
      ]
    },
    {
      "page": "determine_build",
      "title": "Determine build based on reference dataset",
      "topics": [
        "determine_build"
      ]
    },
    {
      "page": "determine_build_biomart",
      "title": "Determines which build a set of SNPs are on",
      "topics": [
        "determine_build_biomart"
      ]
    },
    {
      "page": "determine_build_position",
      "title": "Determine build just from positions",
      "topics": [
        "determine_build_position"
      ]
    },
    {
      "page": "determine_new_datasets",
      "title": "determine_new_datasets",
      "topics": [
        "determine_new_datasets"
      ]
    },
    {
      "page": "ebi_datasets",
      "title": "ebi_datasets",
      "topics": [
        "ebi_datasets"
      ]
    },
    {
      "page": "EbiDataset",
      "title": "Object that downloads, develops and uploads EBI dataset",
      "topics": [
        "EbiDataset"
      ]
    },
    {
      "page": "get_ftp_path",
      "title": "Get harmonised file for specific EBI ID",
      "topics": [
        "get_ftp_path"
      ]
    },
    {
      "page": "get_positions",
      "title": "Lookup positions for given rsids in particular build",
      "topics": [
        "get_positions"
      ]
    },
    {
      "page": "liftover_gwas",
      "title": "Liftover GWAS positions",
      "topics": [
        "liftover_gwas"
      ]
    },
    {
      "page": "listftp",
      "title": "listftp",
      "topics": [
        "listftp"
      ]
    }
  ],
  "_readme": "https://github.com/MRCIEU/GwasDataImport/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",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicRanges",
    "glue",
    "hms",
    "httr",
    "httr2",
    "ieugwasr",
    "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": "liftover.Rmd",
      "filename": "liftover.html",
      "title": "Automating liftover",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2020-06-05 20:11:02",
      "modified": "2023-05-01 21:33:34",
      "commits": 5
    },
    {
      "source": "ebi_workflow.Rmd",
      "filename": "ebi_workflow.html",
      "title": "EBI upload pipeline",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Objectives",
        "Complete workflow for one dataset",
        "Running each step individually",
        "Workflow for all datasets",
        "Lookup build",
        "Suhre proteins",
        "EBI Ignore list"
      ],
      "created": "2020-05-30 08:45:57",
      "modified": "2023-05-01 21:33:34",
      "commits": 6
    },
    {
      "source": "edit.Rmd",
      "filename": "edit.html",
      "title": "Edit existing GWAS meta data",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2020-06-06 14:43:26",
      "modified": "2023-05-01 21:33:34",
      "commits": 2
    },
    {
      "source": "import_pipeline.Rmd",
      "filename": "import_pipeline.html",
      "title": "Importing datasets into OpenGWAS",
      "engine": "knitr::rmarkdown",
      "headings": [
        "As a Contributor",
        "Prerequisites",
        "Summary stats file format",
        "OpenGWAS ID",
        "Setup",
        "Upload a single dataset",
        "1. Create metadata (two methods)",
        "1a. Using the web portal",
        "1b. Using R/GwasDataImport alone",
        "2. Modify the metadata (only when necessary)",
        "3. Format the file and upload for QC",
        "4. Check QC pipeline state and report, and submit for approval",
        "Upload in bulk",
        "What's next",
        "Known issues"
      ],
      "created": "2020-05-30 08:45:57",
      "modified": "2026-02-17 12:22:21",
      "commits": 24
    },
    {
      "source": "import_pipeline_deprecated.Rmd",
      "filename": "import_pipeline_deprecated.html",
      "title": "Importing datasets into OpenGWAS [DEPRECATED]",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Download the summary dataset",
        "2. Initialise",
        "3. Specify columns in dataset",
        "4. Input the meta-data",
        "5. Check that the meta-data are correct",
        "6. Process the summary dataset",
        "6. Upload meta-data",
        "7. Upload processed summary dataset",
        "8. Wait for the API pipeline to convert to VCF format, annotate and create a report",
        "Summary",
        "Example"
      ],
      "created": "2026-02-16 12:53:14",
      "modified": "2026-02-16 12:53:14",
      "commits": 1
    },
    {
      "source": "get_positions.Rmd",
      "filename": "get_positions.html",
      "title": "Looking up chromosome and position for large sets of rs IDs",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-02-23 23:16:54",
      "modified": "2023-05-01 21:33:34",
      "commits": 2
    },
    {
      "source": "testrun.Rmd",
      "filename": "testrun.html",
      "title": "Test run for upload system",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-02-23 23:16:54",
      "modified": "2023-05-01 21:33:34",
      "commits": 2
    }
  ],
  "_score": 5.054613054556888,
  "_indexed": true,
  "_nocasepkg": "gwasdataimport",
  "_universes": [
    "mrcieu",
    "explodecomputer"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-29T19:40:29.000Z",
      "distro": "noble",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "71d8f629997760e64aad0f13e041935109dca7447ac871bc48cfedd397dac671",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-29T19:40:35.000Z",
      "distro": "noble",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "19648bf22384f59193e4fabf1db040e9791fbf09fa628b787daf37bde1036a0b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-29T19:46:57.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "afd9799035afa46e1cabe5644dc686191e59215dc891353c7f8faf0778692f14",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-29T19:47:48.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "757dee2b42bc0835d2591e3c47c7387ea9acde73eeeb031377488b70db007859",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.1",
      "date": "2026-05-29T19:40:47.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "13e9bfffe65a4d40af71fbc58ce588e2691459dc967a47e2e88dd311572781bf",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-29T19:39:10.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "f57ae12c448511c5080c3ea7b4e037df8d6995e54792a5a0ae811a2174b4503c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-29T19:39:10.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "8ba80926fb9a3a3d874bf0ba19a1ce0a111cdb59f265dece5a1ef36c3fa22ee6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-29T19:39:12.000Z",
      "commit": "91c27f37aa116442b125fd054c3cef3ad14a8266",
      "fileid": "604c4b765af20c67ee80912c76c6e7448a4f86f0c26154cf52d54ca08c0e0a1a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26657946910"
    }
  ]
}