{
  "_id": "6a1f2a43b401979e734246ce",
  "Package": "gwasglue",
  "Title": "GWAS summary data sources connected to analytical tools",
  "Version": "0.0.0.9001",
  "Authors@R": "person(\"Gibran\", \"Hemani\", , \"g.hemani@bristol.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0920-1055\"))",
  "Description": "Many tools exist that use GWAS summary data for\ncolocalisation, fine mapping, Mendelian randomization,\nvisualisation, etc. This package is a conduit that connects R\npackages that can retrieve GWAS summary data to various tools\nfor analysing those data.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/mrcieu/gwasglue",
  "BugReports": "https://github.com/mrcieu/gwasglue/issues",
  "VignetteBuilder": "knitr",
  "Remotes": [
    "MRCIEU/genetics.binaRies",
    "mrcieu/gwasvcf",
    "mrcieu/TwoSampleMR",
    "variani/finemapr"
  ],
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libsqlite3-dev\nxz-utils zlib1g-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2025-09-07 06:43:18 UTC",
  "RemoteUrl": "https://github.com/remlapmot/gwasglue",
  "RemoteRef": "fixes",
  "RemoteSha": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-15 16:23:50 UTC",
    "User": "root"
  },
  "Author": "Gibran Hemani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0920-1055>)",
  "Maintainer": "Gibran Hemani <g.hemani@bristol.ac.uk>",
  "MD5sum": "937934bf67102ac185973124d204a1a0",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "gwasglue_0.0.0.9001.tar.gz",
  "_fileid": "f235d7d65f4fa28bb8c01b83e1b3ca9d8d819eccbb831acc76c154ef9095630a",
  "_filesize": 5303419,
  "_sha256": "f235d7d65f4fa28bb8c01b83e1b3ca9d8d819eccbb831acc76c154ef9095630a",
  "_created": "2026-05-15T16:23:50.000Z",
  "_published": "2026-06-02T19:08:50.996Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79150740389,
      "time": 190,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7021677300"
    },
    {
      "job": 79150740614,
      "time": 212,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7021683943"
    },
    {
      "job": 79150740332,
      "time": 122,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7021656479"
    },
    {
      "job": 79150740555,
      "time": 137,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7021661248"
    },
    {
      "job": 79150739540,
      "time": 341,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7021617068"
    },
    {
      "job": 79150739584,
      "time": 176,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7367335619"
    },
    {
      "job": 79150740271,
      "time": 125,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7021657744"
    },
    {
      "job": 79150740779,
      "time": 129,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7021659333"
    },
    {
      "job": 79150740538,
      "time": 170,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7021671229"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/remlapmot/gwasglue",
  "_commit": {
    "id": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
    "author": "Tom Palmer <remlapmot@hotmail.com>",
    "committer": "Tom Palmer <remlapmot@hotmail.com>",
    "message": "Bump roxygen2\n",
    "time": 1757227398
  },
  "_maintainer": {
    "name": "Gibran Hemani",
    "email": "g.hemani@bristol.ac.uk",
    "login": "explodecomputer",
    "uuid": 1924940,
    "orcid": "0000-0003-0920-1055"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "genetics.binaRies",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "gwasvcf",
      "role": "Imports"
    },
    {
      "package": "ieugwasr",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "susieR",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "TwoSampleMR",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "coloc",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "finemapr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "remlapmot",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-31",
      "n": 23
    },
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-36",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "explodecomputer",
      "count": 63,
      "uuid": 1924940
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gwasglue"
  },
  "_devurl": "https://github.com/mrcieu/gwasglue",
  "_searchresults": 142,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gwasglue.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "%>%",
    "clump_gwasvcf",
    "cojo_cond",
    "cojo_sumstat_file",
    "coloc_to_gassocplot",
    "gwasvcf_to_coloc",
    "gwasvcf_to_finemapr",
    "gwasvcf_to_TwoSampleMR",
    "harmonise",
    "harmonise_against_ref",
    "ieugwasr_to_coloc",
    "ieugwasr_to_finemapr",
    "ieugwasr_to_gassocplot",
    "ieugwasr_to_TwoSampleMR",
    "is_forward_strand",
    "make_TwoSampleMR_dat",
    "map_variants_to_regions",
    "pwcoco",
    "read_gwas",
    "read_reference",
    "set_bc4_files",
    "susieR_pipeline",
    "write_out"
  ],
  "_help": [
    {
      "page": "clump_gwasvcf",
      "title": "Perform LD clumping",
      "topics": [
        "clump_gwasvcf"
      ]
    },
    {
      "page": "cojo_cond",
      "title": "Perform conditional analysis using GCTA COJO",
      "topics": [
        "cojo_cond"
      ]
    },
    {
      "page": "cojo_sumstat_file",
      "title": "Write vcf file to cojo sumstat file",
      "topics": [
        "cojo_sumstat_file"
      ]
    },
    {
      "page": "coloc_to_gassocplot",
      "title": "Convert coloc dataset to gassocplot dataset",
      "topics": [
        "coloc_to_gassocplot"
      ]
    },
    {
      "page": "gwasvcf_to_coloc",
      "title": "Generate coloc dataset from vcf files",
      "topics": [
        "gwasvcf_to_coloc"
      ]
    },
    {
      "page": "gwasvcf_to_finemapr",
      "title": "Generate data for fine mapping analysis",
      "topics": [
        "gwasvcf_to_finemapr"
      ]
    },
    {
      "page": "gwasvcf_to_pwcoco",
      "title": "Write files for PWCoCo where data are read from two VCF objects or files.",
      "topics": [
        "gwasvcf_to_pwcoco"
      ]
    },
    {
      "page": "gwasvcf_to_TwoSampleMR",
      "title": "Create exposure or outcome data format for TwoSampleMR from vcf",
      "topics": [
        "gwasvcf_to_TwoSampleMR"
      ]
    },
    {
      "page": "harmonise",
      "title": "Generic harmonisation function",
      "topics": [
        "harmonise"
      ]
    },
    {
      "page": "harmonise_against_ref",
      "title": "Harmonise gwas alleles to be same as reference",
      "topics": [
        "harmonise_against_ref"
      ]
    },
    {
      "page": "ieugwasr_to_coloc",
      "title": "Generate coloc dataset from the IEU GWAS database",
      "topics": [
        "ieugwasr_to_coloc"
      ]
    },
    {
      "page": "ieugwasr_to_finemapr",
      "title": "Generate data for analysis in various finemapping methods",
      "topics": [
        "ieugwasr_to_finemapr"
      ]
    },
    {
      "page": "ieugwasr_to_gassocplot",
      "title": "Generate regional plot for ieugwasr",
      "topics": [
        "ieugwasr_to_gassocplot"
      ]
    },
    {
      "page": "ieugwasr_to_pwcoco",
      "title": "Write files for PWCoCo where data are read from the OpenGWAS DB.",
      "topics": [
        "ieugwasr_to_pwcoco"
      ]
    },
    {
      "page": "ieugwasr_to_TwoSampleMR",
      "title": "Convert output from query to TwoSampleMR format",
      "topics": [
        "ieugwasr_to_TwoSampleMR"
      ]
    },
    {
      "page": "is_forward_strand",
      "title": "Check a GWAS dataset against a reference known to be on the forward strand",
      "topics": [
        "is_forward_strand"
      ]
    },
    {
      "page": "make_TwoSampleMR_dat",
      "title": "Create a harmonised dataset from lists of vcf files",
      "topics": [
        "make_TwoSampleMR_dat"
      ]
    },
    {
      "page": "map_variants_to_regions",
      "title": "For a set of variants map to LD regions",
      "topics": [
        "map_variants_to_regions"
      ]
    },
    {
      "page": "organise_ids",
      "title": "Figure out specific files and IDs depending on what files exist and whethet vcfdir is set",
      "topics": [
        "organise_ids"
      ]
    },
    {
      "page": "pwcoco",
      "title": "Perform pair-wise conditional and colocalisation analysis using PWCoCo",
      "topics": [
        "pwcoco"
      ]
    },
    {
      "page": "read_gwas",
      "title": "Read in GWAS dataset",
      "topics": [
        "read_gwas"
      ]
    },
    {
      "page": "read_reference",
      "title": "Read in reference dataset",
      "topics": [
        "read_reference"
      ]
    },
    {
      "page": "set_bc4_files",
      "title": "Determine locations of useful reference datasets on bluecrystal4",
      "topics": [
        "set_bc4_files"
      ]
    },
    {
      "page": "susieR_pipeline",
      "title": "Perform fine mapping pipeline using susieR",
      "topics": [
        "susieR_pipeline"
      ]
    },
    {
      "page": "write_out",
      "title": "Create format for HPC pipeline",
      "topics": [
        "write_out"
      ]
    }
  ],
  "_readme": "https://github.com/remlapmot/gwasglue/raw/fixes/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "genetics.binaRies",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glmnet",
    "glue",
    "GPArotation",
    "gridExtra",
    "gtable",
    "gwasglue2",
    "gwasvcf",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "ieugwasr",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "mixsqp",
    "mnormt",
    "MRMix",
    "MRPRESSO",
    "nlme",
    "openssl",
    "otel",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "promises",
    "psych",
    "purrr",
    "R6",
    "RadialMR",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RCurl",
    "reshape",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "susieR",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "TwoSampleMR",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "finemapping.Rmd",
      "filename": "finemapping.html",
      "title": "Clumping and finemapping",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Clumping",
        "Data from OpenGWAS",
        "Data from VCF",
        "Finemapping",
        "Finemapping across the whole dataset",
        "Multi-population finemapping"
      ],
      "created": "2019-11-06 12:19:45",
      "modified": "2021-04-12 18:10:09",
      "commits": 4
    },
    {
      "source": "cojo.Rmd",
      "filename": "cojo.html",
      "title": "Conditional analysis of VCF files",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Finemapping pipeline",
        "Conditional analysis pipeline"
      ],
      "created": "2020-07-07 21:39:42",
      "modified": "2020-07-09 00:22:45",
      "commits": 3
    },
    {
      "source": "finemapping_experiment.Rmd",
      "filename": "finemapping_experiment.html",
      "title": "Finemapping experiments",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-04-12 18:10:09",
      "modified": "2021-04-12 18:10:09",
      "commits": 1
    },
    {
      "source": "ld_ref.Rmd",
      "filename": "ld_ref.html",
      "title": "Generate LD matrices",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-02-24 01:01:37",
      "modified": "2025-08-01 10:24:16",
      "commits": 2
    },
    {
      "source": "colocalisation.Rmd",
      "filename": "colocalisation.html",
      "title": "Genetic colocalisation",
      "engine": "knitr::rmarkdown",
      "headings": [
        "ieugwasr",
        "gwasvcf"
      ],
      "created": "2019-11-06 12:19:45",
      "modified": "2025-08-01 10:22:43",
      "commits": 5
    },
    {
      "source": "gwas2020.Rmd",
      "filename": "gwas2020.html",
      "title": "Major changes to the IEU GWAS resources for 2020",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What has changed",
        "Dataset IDs",
        "Authentication",
        "UKBiobank data has been curated",
        "All data is now harmonised",
        "LD reference panel is now harmonised",
        "Instrument lists are up-to-date",
        "dbSNP rs IDs",
        "Everything is faster",
        "What is new",
        "Browse available datasets online",
        "Chromosome and position",
        "INDELs are retained",
        "Multi-allelic variants are retained",
        "More data",
        "Error messages are more informative",
        "Easier programmatic access to the database",
        "Local LD operations",
        "Access the data directly",
        "Connect the data to different analytical tools",
        "Key links",
        "How to request new data"
      ],
      "created": "2020-01-07 13:57:33",
      "modified": "2020-01-11 20:28:41",
      "commits": 3
    },
    {
      "source": "mr.Rmd",
      "filename": "mr.html",
      "title": "Mendelian randomization",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Using TwoSampleMR",
        "Using GWAS VCF files",
        "Other options",
        "Clumping vcf files",
        "Extracting outcome data with LD proxies",
        "Further MR methods",
        "Bluecrystal4 users"
      ],
      "created": "2019-11-06 12:19:45",
      "modified": "2025-08-01 10:24:23",
      "commits": 6
    }
  ],
  "_score": 5.173477643452995,
  "_indexed": false,
  "_nocasepkg": "gwasglue",
  "_universes": [
    "mrcieu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:26:48.000Z",
      "distro": "noble",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "b09b6878978351f1ca4b3b574f0565796e49a3ddd3149563a7ac15ed3e847b05",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:27:07.000Z",
      "distro": "noble",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "fd1d35044d418f936242f393c0083bf4dcdb4613ed7a9cded9d044e7e93592f5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:25:47.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "8b5834d371acdb9f4a75ca083ecb9eb81073c8464c4ccf86b381b56e9769395b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:26:00.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "af4e712210c1c402e242efa9ad5fc1d7022c57839ecc3bbe75e7aac0f5b847d1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:25:45.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "24da2a3008982ec1393b15ee5a5523b4e96b1614c4afb35ed3f1f454fc74b319",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:25:45.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "80fda1cd312ce1015293a1d26243305fb3fc1f03522f3c29d9ba4c6ade697050",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9001",
      "date": "2026-05-15T16:26:22.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "7145055c8c78c7f00c6f4421af6116d52ba9c4bd0b136cb69290005485d5281d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.0.9001",
      "date": "2026-06-02T19:08:33.000Z",
      "commit": "7fa098bfbaeb3b14477af8634a20af5b3cf1cde8",
      "fileid": "6fb02a868d0545ba08e11a83759adc712e70603e5d63ed19bd46402b6a06bdca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/25928582462"
    }
  ]
}