{ "_id": "6a1ad26c1d7bb097a09e2eeb", "Package": "MungeSumstats", "Type": "Package", "Title": "Standardise summary statistics from GWAS", "Version": "1.21.0", "Authors@R": "c(person(given = \"Alan\",\nfamily = \"Murphy\",\nrole = c(\"aut\",\"cre\"),\nemail = \"alanmurph94@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-2487-8753\")),\nperson(given = \"Brian\",\nfamily = \"Schilder\",\nrole = c(\"aut\",\"ctb\"),\nemail = \"brian_schilder@alumni.brown.edu\",\ncomment = c(ORCID = \"0000-0001-5949-2191\")),\nperson(given = \"Nathan\",\nfamily = \"Skene\",\nrole = c(\"aut\"),\nemail = \"nathan.skene@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6807-3180\")))", "Description": "The *MungeSumstats* package is designed to facilitate the\nstandardisation of GWAS summary statistics. It reformats\ninputted summary statisitics to include SNP, CHR, BP and can\nlook up these values if any are missing. It also pefrorms\ndozens of QC and filtering steps to ensure high data quality\nand minimise inter-study differences.", "URL": "https://github.com/neurogenomics/MungeSumstats,\nhttps://al-murphy.github.io/MungeSumstats/", "BugReports": "https://github.com/neurogenomics/MungeSumstats/issues", "License": "Artistic-2.0", "biocViews": "SNP, WholeGenome, Genetics, ComparativeGenomics,\nGenomeWideAssociation, GenomicVariation, Preprocessing", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:42 UTC", "RemoteUrl": "https://github.com/bioc/MungeSumstats", "RemoteRef": "HEAD", "RemoteSha": "d3c05cb3f843b95108ee5e817398f562fe5ee705", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:47:57 UTC", "User": "root" }, "Author": "Alan Murphy [aut, cre] (ORCID: ),\nBrian Schilder [aut, ctb] (ORCID:\n),\nNathan Skene [aut] (ORCID: )", "Maintainer": "Alan Murphy ", "MD5sum": "cf8e6cb0140881135c0564595d362ed6", "_user": "bioc", "_type": "src", "_file": "MungeSumstats_1.21.0.tar.gz", "_fileid": "d61a214e1c5acc53baa5ba4028b26a5bd4a518ac2c1e054cfaa1361ee83317ad", "_filesize": 2055639, "_sha256": "d61a214e1c5acc53baa5ba4028b26a5bd4a518ac2c1e054cfaa1361ee83317ad", "_created": "2026-05-30T07:47:57.000Z", "_published": "2026-05-30T12:05:00.498Z", "_jobs": [ { "job": 78634561301, "time": 436, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306638464" }, { "job": 78634561302, "time": 938, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7306688532" }, { "job": 78634561304, "time": 1104, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306704356" }, { "job": 78634561303, "time": 2799, "config": 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N can also be inputted with \"ldsc\", \"sum\", \"giant\" or \"metal\" by passing one or multiple of these.", "topics": [ "compute_nsize" ] }, { "page": "download_vcf", "title": "Download VCF file and its index file from Open GWAS", "topics": [ "download_vcf" ] }, { "page": "find_sumstats", "title": "Search Open GWAS for datasets matching criteria", "topics": [ "find_sumstats" ] }, { "page": "format_sumstats", "title": "Check that summary statistics from GWAS are in a homogeneous format", "topics": [ "format_sumstats" ] }, { "page": "formatted_example", "title": "Formatted example", "topics": [ "formatted_example" ] }, { "page": "get_eff_frq_allele_combns", "title": "Get combinations of uncorrected allele and effect (and frq) columns", "topics": [ "get_eff_frq_allele_combns" ] }, { "page": "get_genome_builds", "title": "Infer genome builds", "topics": [ "get_genome_builds" ] }, { "page": "hg19ToHg38", "title": "UCSC Chain file hg19 to hg38", "topics": [ "hg19ToHg38" ] }, { "page": "hg38ToHg19", "title": "UCSC Chain file hg38 to hg19", "topics": [ "hg38ToHg19" ] }, { "page": "ieu-a-298", "title": "Local ieu-a-298 file from IEU Open GWAS", "topics": [ "ieu-a-298" ] }, { "page": "import_sumstats", "title": "Import full genome-wide GWAS summary statistics from Open GWAS", "topics": [ "import_sumstats" ] }, { "page": "index_tabular", "title": "Tabix-index file: table", "concept": [ "tabix" ], "topics": [ "index_tabular" ] }, { "page": "infer_effect_column", "title": "Infer if effect relates to a1 or A2 if ambiguously named", "topics": [ "infer_effect_column" ] }, { "page": "liftover", "title": "Genome build liftover", "topics": [ "liftover" ] }, { "page": "list_sumstats", "title": "List munged summary statistics", "topics": [ "list_sumstats" ] }, { "page": "load_ref_genome_data", "title": "Load the reference genome data for SNPs of interest", "topics": [ "load_ref_genome_data" ] }, { "page": "load_snp_loc_data", "title": "Loads the SNP locations and alleles for Homo sapiens from dbSNP builds", "topics": [ "load_snp_loc_data" ] }, { "page": "parse_logs", "title": "Parse data from log files", "topics": [ "parse_logs" ] }, { "page": "raw_ALSvcf", "title": "GWAS Amyotrophic lateral sclerosis ieu open GWAS project - 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