{
  "_id": "6a494a02f6c47c44194988a5",
  "Package": "SeqVarTools",
  "Version": "1.51.0",
  "Type": "Package",
  "Title": "Tools for variant data",
  "Description": "An interface to the fast-access storage format for VCF\ndata provided in SeqArray, with tools for common operations and\nanalysis.",
  "Author": "Stephanie M. Gogarten, Xiuwen Zheng, Adrienne Stilp",
  "Maintainer": "Stephanie M. Gogarten <sdmorris@uw.edu>",
  "License": "GPL-3",
  "URL": "https://github.com/smgogarten/SeqVarTools",
  "LazyData": "yes",
  "biocViews": "SNP, GeneticVariability, Sequencing, Genetics",
  "Collate": "AllClasses.R AllGenerics.R AllUtilities.R\nMethods-SeqVarGDSClass.R Methods-SeqVarData.R\nMethods-Iterator.R chromWithPAR.R duplicateDiscordance.R hwe.R\ninbreedCoeff.R mendelErr.R pca.R setVariantID.R\nalternateAlleleDetection.R refFrac.R regression.R",
  "Config/pak/sysreqs": "cmake make libicu-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:02 UTC",
  "RemoteUrl": "https://github.com/bioc/SeqVarTools",
  "RemoteRef": "HEAD",
  "RemoteSha": "5402069d60903d04607c9271796ffb5a25cbc263",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 15:17:43 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "SeqVarTools_1.51.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/5534ae5a42ec67497f9fcfb38fa3ece89ca7dd516e11338d5c3f4a47238ce1ec",
  "_filesize": 750969,
  "_sha256": "5534ae5a42ec67497f9fcfb38fa3ece89ca7dd516e11338d5c3f4a47238ce1ec",
  "_expires": "2026-10-12T17:59:28.000Z",
  "_created": "2026-07-03T15:17:43.000Z",
  "_published": "2026-07-04T17:59:30.021Z",
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 17
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720",
  "_status": "failure",
  "_upstream": "https://github.com/bioc/SeqVarTools",
  "_commit": {
    "id": "5402069d60903d04607c9271796ffb5a25cbc263",
    "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",
    "time": 1777379882
  },
  "_maintainer": {
    "name": "Stephanie M. Gogarten",
    "email": "sdmorris@uw.edu",
    "login": "smgogarten",
    "orcid": "0000-0002-7231-9745",
    "description": "Senior research scientist in the Genetic Analysis Center",
    "uuid": 2028958
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85154325409,
      "time": 175,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8070029158"
    },
    {
      "job": 85154325513,
      "time": 297,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8070067506"
    },
    {
      "job": 85154325542,
      "time": 297,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8070067641"
    },
    {
      "job": 85154325570,
      "time": 200,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8070178664"
    },
    {
      "job": 85154325488,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8070164512"
    },
    {
      "job": 85154325193,
      "time": 199,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8069971432"
    },
    {
      "job": 85154325457,
      "time": 157,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8070023484"
    },
    {
      "job": 85154325459,
      "time": 178,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8070030247"
    },
    {
      "job": 85154325486,
      "time": 211,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8070040879"
    },
    {
      "job": 85154325568,
      "time": 164,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8070025723"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "SeqArray",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "gdsfmt",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "GWASExactHW",
      "role": "Imports"
    },
    {
      "package": "logistf",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "snp",
    "geneticvariability",
    "sequencing",
    "genetics"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "smgogarten",
      "count": 74,
      "uuid": 2028958
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "dtenenba",
      "count": 12,
      "uuid": 2286826
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "amstilp",
      "count": 7,
      "uuid": 3944584
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "sonali-bioc",
      "count": 2,
      "uuid": 6373953
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/smgogarten/seqvartools",
  "_searchresults": 551,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SeqVarTools.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/smgogarten/seqvartools",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "alleleCount",
    "alleleDosage",
    "alleleFrequency",
    "altChar",
    "altDosage",
    "alternateAlleleDetection",
    "applyMethod",
    "chromWithPAR",
    "countSingletons",
    "currentRanges",
    "currentVariants",
    "duplicateDiscordance",
    "expandedAltDosage",
    "expandedVariantIndex",
    "getGenotype",
    "getGenotypeAlleles",
    "getVariableLengthData",
    "granges",
    "heterozygosity",
    "hethom",
    "homozygosity",
    "hwe",
    "imputedDosage",
    "inbreedCoeff",
    "isSNV",
    "isVariant",
    "iterateFilter",
    "lastFilter",
    "lastFilter<-",
    "meanBySample",
    "mendelErr",
    "minorAlleleCount",
    "missingGenotypeRate",
    "nAlleles",
    "pca",
    "refChar",
    "refDosage",
    "refFrac",
    "refFracOverHets",
    "refFracPlot",
    "regression",
    "resetIterator",
    "sampleData",
    "sampleData<-",
    "SeqVarBlockIterator",
    "SeqVarData",
    "SeqVarIterator",
    "SeqVarListIterator",
    "SeqVarRangeIterator",
    "SeqVarWindowIterator",
    "setVariantID",
    "show",
    "titv",
    "validateSex",
    "variantBlock",
    "variantData",
    "variantData<-",
    "variantFilter",
    "variantInfo",
    "variantRanges"
  ],
  "_datasets": [
    {
      "name": "pedigree",
      "title": "Pedigree for example data",
      "object": "pedigree",
      "class": [
        "data.frame"
      ],
      "fields": [
        "family",
        "individ",
        "father",
        "mother",
        "sex",
        "sample.id"
      ],
      "rows": 90,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "SeqVarTools-package",
      "title": "Tools for Variant Analysis",
      "topics": [
        "SeqVarTools-package",
        "SeqVarTools"
      ]
    },
    {
      "page": "allele-methods",
      "title": "Extract allele information from a GDS object",
      "topics": [
        "allele-methods",
        "altChar",
        "altChar,SeqVarGDSClass-method",
        "nAlleles",
        "nAlleles,SeqVarGDSClass-method",
        "refChar",
        "refChar,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "alleleFrequency",
      "title": "Allele frequency",
      "topics": [
        "alleleCount",
        "alleleCount,SeqVarData-method",
        "alleleCount,SeqVarGDSClass-method",
        "alleleFrequency",
        "alleleFrequency,SeqVarData-method",
        "alleleFrequency,SeqVarGDSClass-method",
        "minorAlleleCount",
        "minorAlleleCount,SeqVarData-method",
        "minorAlleleCount,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "alternateAlleleDetection",
      "title": "alternateAlleleDetection",
      "topics": [
        "alternateAlleleDetection",
        "alternateAlleleDetection,SeqVarData,SeqVarData-method"
      ]
    },
    {
      "page": "applyMethod",
      "title": "Apply method to GDS object",
      "topics": [
        "applyMethod",
        "applyMethod,SeqVarGDSClass,function,character-method",
        "applyMethod,SeqVarGDSClass,function,GRanges-method",
        "applyMethod,SeqVarGDSClass,function,missing-method",
        "applyMethod,SeqVarGDSClass,function,numeric-method"
      ]
    },
    {
      "page": "chromWithPAR",
      "title": "Identify pseudoautosomal region",
      "topics": [
        "chromWithPAR",
        "chromWithPAR,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "countSingletons",
      "title": "Count singletons",
      "topics": [
        "countSingletons",
        "countSingletons,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "duplicateDiscordance",
      "title": "Duplicate discordance",
      "topics": [
        "duplicateDiscordance",
        "duplicateDiscordance,SeqVarData,missing-method",
        "duplicateDiscordance,SeqVarData,SeqVarData-method",
        "duplicateDiscordance,SeqVarIterator,missing-method"
      ]
    },
    {
      "page": "getGenotype",
      "title": "Get genotype data",
      "topics": [
        "alleleDosage",
        "alleleDosage,SeqVarGDSClass,list-method",
        "alleleDosage,SeqVarGDSClass,numeric-method",
        "altDosage",
        "altDosage,SeqVarGDSClass-method",
        "expandedAltDosage",
        "expandedAltDosage,SeqVarGDSClass-method",
        "getGenotype",
        "getGenotype,SeqVarGDSClass-method",
        "getGenotypeAlleles",
        "getGenotypeAlleles,SeqVarGDSClass-method",
        "refDosage",
        "refDosage,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "getVariableLengthData",
      "title": "Get variable-length data",
      "topics": [
        "getVariableLengthData",
        "getVariableLengthData,SeqVarGDSClass,character-method"
      ]
    },
    {
      "page": "heterozygosity",
      "title": "Heterozygosity and Homozygosity",
      "topics": [
        "heterozygosity",
        "heterozygosity,SeqVarGDSClass-method",
        "hethom",
        "hethom,SeqVarGDSClass-method",
        "homozygosity",
        "homozygosity,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "hwe",
      "title": "Exact test for Hardy-Weinberg equilibrium",
      "topics": [
        "hwe",
        "hwe,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "imputedDosage",
      "title": "Get imputed dosage",
      "topics": [
        "imputedDosage",
        "imputedDosage,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "inbreedCoeff",
      "title": "Inbreeding coefficient",
      "topics": [
        "inbreedCoeff",
        "inbreedCoeff,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "isSNV",
      "title": "Flag single nucleotide variants",
      "topics": [
        "isSNV",
        "isSNV,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "isVariant",
      "title": "Locate variant samples across sites",
      "topics": [
        "isVariant",
        "isVariant,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "Iterator-class",
      "title": "Iterators",
      "topics": [
        "currentRanges",
        "currentRanges,SeqVarBlockIterator-method",
        "currentRanges,SeqVarListIterator-method",
        "currentRanges,SeqVarRangeIterator-method",
        "currentVariants",
        "currentVariants,SeqVarBlockIterator-method",
        "currentVariants,SeqVarIterator-method",
        "iterateFilter",
        "iterateFilter,SeqVarIterator-method",
        "lastFilter",
        "lastFilter,SeqVarIterator-method",
        "lastFilter<-",
        "lastFilter<-,SeqVarIterator,numeric-method",
        "resetIterator",
        "resetIterator,SeqVarIterator-method",
        "SeqVarBlockIterator",
        "SeqVarBlockIterator-class",
        "SeqVarIterator",
        "SeqVarIterator-class",
        "SeqVarListIterator",
        "SeqVarListIterator-class",
        "SeqVarRangeIterator",
        "SeqVarRangeIterator-class",
        "SeqVarWindowIterator",
        "SeqVarWindowIterator-class",
        "show,SeqVarIterator-method",
        "show,SeqVarListIterator-method",
        "show,SeqVarRangeIterator-method",
        "variantBlock",
        "variantBlock,SeqVarBlockIterator-method",
        "variantFilter",
        "variantFilter,SeqVarIterator-method",
        "variantRanges",
        "variantRanges,SeqVarListIterator-method",
        "variantRanges,SeqVarRangeIterator-method"
      ]
    },
    {
      "page": "meanBySample",
      "title": "Mean value by sample",
      "topics": [
        "meanBySample",
        "meanBySample,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "mendelErr",
      "title": "Mendelian errors",
      "topics": [
        "mendelErr",
        "mendelErr,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "missingGenotypeRate",
      "title": "Missing genotype rate",
      "topics": [
        "missingGenotypeRate",
        "missingGenotypeRate,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "pca",
      "title": "Principal Component Analysis",
      "topics": [
        "pca",
        "pca,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "pedigree",
      "title": "Pedigree for example data",
      "topics": [
        "pedigree"
      ]
    },
    {
      "page": "refFrac",
      "title": "Reference allele fraction",
      "topics": [
        "refFrac",
        "refFrac,SeqVarGDSClass-method",
        "refFracOverHets",
        "refFracOverHets,SeqVarGDSClass-method",
        "refFracPlot",
        "refFracPlot,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "regression",
      "title": "Linear or logistic regression",
      "topics": [
        "regression",
        "regression,SeqVarData-method"
      ]
    },
    {
      "page": "SeqVarData-class",
      "title": "SeqVarData",
      "topics": [
        "granges",
        "granges,SeqVarData-method",
        "sampleData",
        "sampleData,SeqVarData-method",
        "sampleData<-",
        "sampleData<-,SeqVarData,AnnotatedDataFrame-method",
        "SeqVarData",
        "SeqVarData-class",
        "show,SeqVarData-method",
        "validateSex",
        "validateSex,SeqVarData-method",
        "variantData",
        "variantData,SeqVarData-method",
        "variantData<-",
        "variantData<-,SeqVarData,AnnotatedDataFrame-method"
      ]
    },
    {
      "page": "setVariantID",
      "title": "Change the variant ID of a GDS file",
      "topics": [
        "setVariantID"
      ]
    },
    {
      "page": "titv",
      "title": "Transition/Transversion Ratio",
      "topics": [
        "titv",
        "titv,SeqVarGDSClass-method"
      ]
    },
    {
      "page": "variantInfo",
      "title": "Variant info",
      "topics": [
        "expandedVariantIndex",
        "expandedVariantIndex,SeqVarGDSClass-method",
        "variantInfo",
        "variantInfo,SeqVarGDSClass-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SeqVarTools/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "boot",
    "broom",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "digest",
    "dplyr",
    "forcats",
    "foreach",
    "formula.tools",
    "gdsfmt",
    "generics",
    "GenomicRanges",
    "glmnet",
    "glue",
    "GWASExactHW",
    "haven",
    "hms",
    "IRanges",
    "iterators",
    "jomo",
    "lattice",
    "lifecycle",
    "lme4",
    "logistf",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "mice",
    "minqa",
    "mitml",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "operator.tools",
    "ordinal",
    "pan",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rbibutils",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "rpart",
    "S4Vectors",
    "SeqArray",
    "Seqinfo",
    "shape",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "ucminf",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XVector"
  ],
  "_score": 7.44358213529731,
  "_indexed": true,
  "_nocasepkg": "seqvartools",
  "_universes": [
    "bioc",
    "smgogarten"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-07-03T15:21:27.000Z",
      "distro": "resolute",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/c34773d6bd70fd8b10fc4a8ef6f957987c8343c3fab175a036beec1c56617773",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-07-03T15:21:24.000Z",
      "distro": "resolute",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/0da75a903e1f39f745a71841217f2fcb7ee00ad7e4374fe69ce7ab1d12002016",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-07-03T15:27:30.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/9943672b73935b59e70881e9ba55c8c93d32e60add45935fb7e5aa3019c4d225",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-07-03T15:27:15.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/f2ba1f2347f6d0c3f0d744a8ecb050415d7acd7ca05449e732d6b5ed1d5f9b8d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.51.0",
      "date": "2026-07-03T15:20:43.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/7f6e4cd0b53bc1c785c0640e83bdc0a1873bc8ad75639ba92888f2d02912be47",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-07-03T15:19:21.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/9f25d143594a4dc03cbd9e92c1124279478ac7ed5c2ef2d10dce5e751887c940",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-07-03T15:19:17.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/981474e3655f6be6c2393c04e23a25415b0093210b213de12751250873d032f3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-07-03T15:19:10.000Z",
      "commit": "5402069d60903d04607c9271796ffb5a25cbc263",
      "fileid": "https://r2.ropensci.org/8d5e9dab789e20ddb590f03304461956348c6fa69c362a30e3dbc5e2dbc282b3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28669185720"
    }
  ]
}