{
  "_id": "6a1f38b9b401979e73428e27",
  "Package": "HIBAG",
  "Type": "Package",
  "Title": "HLA Genotype Imputation with Attribute Bagging",
  "Version": "1.49.0",
  "Date": "2026-04-24",
  "Authors@R": "c(person(\"Xiuwen\", \"Zheng\", role=c(\"aut\", \"cre\", \"cph\"),\nemail=\"zhengx@u.washington.edu\", comment=c(ORCID=\"0000-0002-1390-0708\")),\nperson(\"Bruce\", \"Weir\", role=c(\"ctb\", \"ths\"),\nemail=\"bsweir@u.washington.edu\", comment=c(ORCID=\"0000-0002-4883-1247\")))",
  "Description": "Imputes HLA classical alleles using GWAS SNP data, and it\nrelies on a training set of HLA and SNP genotypes. HIBAG can be\nused by researchers with published parameter estimates instead\nof requiring access to large training sample datasets. It\ncombines the concepts of attribute bagging, an ensemble\nclassifier method, with haplotype inference for SNPs and HLA\ntypes. Attribute bagging is a technique which improves the\naccuracy and stability of classifier ensembles using bootstrap\naggregating and random variable selection.",
  "License": "GPL-3",
  "LazyData": "yes",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "GNU make",
  "ByteCompile": "TRUE",
  "biocViews": "Genetics, StatisticalMethod",
  "URL": "https://github.com/zhengxwen/HIBAG,\nhttps://hibag.s3.amazonaws.com/index.html",
  "Config/pak/sysreqs": "make",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:33 UTC",
  "RemoteUrl": "https://github.com/bioc/HIBAG",
  "RemoteRef": "HEAD",
  "RemoteSha": "ea64e9b83517845893aa2b7fad093856471680e0",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-11 10:06:55 UTC",
    "User": "root"
  },
  "Author": "Xiuwen Zheng [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-1390-0708>),\nBruce Weir [ctb, ths] (ORCID: <https://orcid.org/0000-0002-4883-1247>)",
  "Maintainer": "Xiuwen Zheng <zhengx@u.washington.edu>",
  "MD5sum": "017b6b33a00fafc84270fead68931c0c",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-11T10:06:55.000Z",
  "_published": "2026-06-02T20:10:33.651Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25663524037",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/HIBAG",
  "_commit": {
    "id": "ea64e9b83517845893aa2b7fad093856471680e0",
    "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": 1777380033
  },
  "_maintainer": {
    "name": "Xiuwen Zheng",
    "email": "zhengx@u.washington.edu",
    "orcid": "0000-0002-1390-0708"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.0",
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    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.0",
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    {
      "package": "methods",
      "role": "Imports"
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    {
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    {
      "package": "parallel",
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      "package": "ggplot2",
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    {
      "package": "reshape2",
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    {
      "package": "gdsfmt",
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    {
      "package": "SNPRelate",
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    {
      "package": "SeqArray",
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      "package": "knitr",
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    {
      "package": "Rsamtools",
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-16",
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    {
      "week": "2026-17",
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  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "statisticalmethod",
    "bioinformatics",
    "gpu",
    "hla",
    "imputation",
    "mhc",
    "snp",
    "cpp"
  ],
  "_stars": 31,
  "_contributors": [
    {
      "user": "zhengxwen",
      "count": 484,
      "uuid": 6189013
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 548,
    "source": "https://www.bioconductor.org/packages/stats/bioc/HIBAG"
  },
  "_mentions": 22,
  "_devurl": "https://github.com/zhengxwen/hibag",
  "_searchresults": 56,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HIBAG.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/zhengxwen/hibag",
  "_realowner": "bioc",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.9.1",
      "date": "2012-06-21"
    },
    {
      "version": "0.9.2",
      "date": "2012-08-05"
    },
    {
      "version": "0.9.3",
      "date": "2012-10-20"
    },
    {
      "version": "0.9.4",
      "date": "2012-12-22"
    },
    {
      "version": "1.0.0",
      "date": "2013-03-26"
    },
    {
      "version": "1.1.0",
      "date": "2013-06-04"
    },
    {
      "version": "1.2.0",
      "date": "2013-07-29"
    },
    {
      "version": "1.2.0.1",
      "date": "2013-08-12"
    },
    {
      "version": "1.2.1",
      "date": "2013-10-30"
    },
    {
      "version": "1.2.2",
      "date": "2013-12-21"
    },
    {
      "version": "1.2.3",
      "date": "2014-03-06"
    },
    {
      "version": "1.2.4",
      "date": "2014-10-03"
    }
  ],
  "_exports": [
    "hlaAllele",
    "hlaAlleleDigit",
    "hlaAlleleSubset",
    "hlaAlleleToVCF",
    "hlaAssocTest",
    "hlaAssocTest.hlaAASeqClass",
    "hlaAssocTest.hlaAlleleClass",
    "hlaAttrBagging",
    "hlaBED2Geno",
    "hlaCheckAllele",
    "hlaCheckSNPs",
    "hlaClose",
    "hlaCombineAllele",
    "hlaCombineModelObj",
    "hlaCompareAllele",
    "hlaConvSequence",
    "hlaDistance",
    "hlaFlankingSNP",
    "hlaGDS2Geno",
    "hlaGeno2PED",
    "hlaGenoAFreq",
    "hlaGenoCombine",
    "hlaGenoLD",
    "hlaGenoMFreq",
    "hlaGenoMRate",
    "hlaGenoMRate_Samp",
    "hlaGenoSubset",
    "hlaGenoSubsetFlank",
    "hlaGenoSwitchStrand",
    "hlaLDMatrix",
    "hlaLociInfo",
    "hlaMakeSNPGeno",
    "hlaModelFiles",
    "hlaModelFromObj",
    "hlaModelToObj",
    "hlaOutOfBag",
    "hlaParallelAttrBagging",
    "hlaPredict",
    "hlaPredMerge",
    "hlaPublish",
    "hlaReport",
    "hlaReportPlot",
    "hlaSampleAllele",
    "hlaSetKernelTarget",
    "hlaSNPID",
    "hlaSplitAllele",
    "hlaSubModelObj",
    "hlaUniqueAllele",
    "plot.hlaAttrBagClass",
    "plot.hlaAttrBagObj",
    "predict.hlaAttrBagClass",
    "print.hlaAlleleClass",
    "print.hlaAttrBagClass",
    "print.hlaAttrBagObj",
    "print.hlaSNPGenoClass",
    "summary.hlaAASeqClass",
    "summary.hlaAlleleClass",
    "summary.hlaAttrBagClass",
    "summary.hlaAttrBagObj",
    "summary.hlaSNPGenoClass"
  ],
  "_datasets": [
    {
      "name": "HapMap_CEU_Geno",
      "title": "SNP genotypes of a study simulated from HapMap CEU genotypic data",
      "object": "HapMap_CEU_Geno",
      "class": [
        "hlaSNPGenoClass"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HLA_Type_Table",
      "title": "Four-digit HLA types of a study simulated from HapMap CEU",
      "object": "HLA_Type_Table",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample.id",
        "A.1",
        "A.2",
        "B.1",
        "B.2",
        "C.1",
        "C.2",
        "DQA1.1",
        "DQA1.2",
        "DQB1.1",
        "DQB1.2",
        "DRB1.1",
        "DRB1.2"
      ],
      "rows": 60,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "HIBAG-package",
      "title": "HLA Genotype Imputation with Attribute Bagging",
      "topics": [
        "HIBAG-package",
        "HIBAG"
      ]
    },
    {
      "page": "HapMap_CEU_Geno",
      "title": "SNP genotypes of a study simulated from HapMap CEU genotypic data",
      "topics": [
        "HapMap_CEU_Geno"
      ]
    },
    {
      "page": "HLA_Type_Table",
      "title": "Four-digit HLA types of a study simulated from HapMap CEU",
      "topics": [
        "HLA_Type_Table"
      ]
    },
    {
      "page": "hlaAASeqClass",
      "title": "Class of HLA Amino Acid Sequence Type",
      "topics": [
        "hlaAASeqClass"
      ]
    },
    {
      "page": "hlaAllele",
      "title": "A list of HLA/KIR types",
      "topics": [
        "hlaAllele"
      ]
    },
    {
      "page": "hlaAlleleClass",
      "title": "Class of HLA/KIR Type",
      "topics": [
        "hlaAlleleClass"
      ]
    },
    {
      "page": "hlaAlleleDigit",
      "title": "Trim HLA alleles",
      "topics": [
        "hlaAlleleDigit"
      ]
    },
    {
      "page": "hlaAlleleSubset",
      "title": "Get a subset of HLA/KIR types",
      "topics": [
        "hlaAlleleSubset"
      ]
    },
    {
      "page": "hlaAlleleToVCF",
      "title": "Convert HLA alleles to VCF",
      "topics": [
        "hlaAlleleToVCF"
      ]
    },
    {
      "page": "hlaAssocTest",
      "title": "Statistical Association Tests",
      "topics": [
        "hlaAssocTest",
        "hlaAssocTest.hlaAASeqClass",
        "hlaAssocTest.hlaAlleleClass"
      ]
    },
    {
      "page": "hlaAttrBagClass",
      "title": "The class of HIBAG model",
      "topics": [
        "hlaAttrBagClass"
      ]
    },
    {
      "page": "hlaAttrBagging",
      "title": "Build a HIBAG model",
      "topics": [
        "hlaAttrBagging"
      ]
    },
    {
      "page": "hlaAttrBagObj",
      "title": "The class of HIBAG object",
      "topics": [
        "hlaAttrBagObj"
      ]
    },
    {
      "page": "hlaBED2Geno",
      "title": "Convert from PLINK BED format",
      "topics": [
        "hlaBED2Geno"
      ]
    },
    {
      "page": "hlaCheckAllele",
      "title": "Check SNP alleles",
      "topics": [
        "hlaCheckAllele"
      ]
    },
    {
      "page": "hlaCheckSNPs",
      "title": "Check the SNP predictors in a HIBAG model",
      "topics": [
        "hlaCheckSNPs"
      ]
    },
    {
      "page": "hlaClose",
      "title": "Dispose a model object",
      "topics": [
        "hlaClose"
      ]
    },
    {
      "page": "hlaCombineAllele",
      "title": "Combine two datasets of HLA types",
      "topics": [
        "hlaCombineAllele"
      ]
    },
    {
      "page": "hlaCombineModelObj",
      "title": "Combine two HIBAG models together",
      "topics": [
        "hlaCombineModelObj"
      ]
    },
    {
      "page": "hlaCompareAllele",
      "title": "Evaluate prediction accuracies",
      "topics": [
        "hlaCompareAllele"
      ]
    },
    {
      "page": "hlaConvSequence",
      "title": "Conversion From HLA Alleles to Amino Acid Sequences",
      "topics": [
        "hlaConvSequence"
      ]
    },
    {
      "page": "hlaDistance",
      "title": "Distance matrix of HLA alleles",
      "topics": [
        "hlaDistance"
      ]
    },
    {
      "page": "hlaFlankingSNP",
      "title": "SNP IDs or SNP genotypes in Flanking Region",
      "topics": [
        "hlaFlankingSNP",
        "hlaGenoSubsetFlank"
      ]
    },
    {
      "page": "hlaGDS2Geno",
      "title": "Import genotypes from a GDS file",
      "topics": [
        "hlaGDS2Geno"
      ]
    },
    {
      "page": "hlaGeno2PED",
      "title": "Convert to PLINK PED format",
      "topics": [
        "hlaGeno2PED"
      ]
    },
    {
      "page": "hlaGenoAFreq",
      "title": "Allele Frequency",
      "topics": [
        "hlaGenoAFreq"
      ]
    },
    {
      "page": "hlaGenoCombine",
      "title": "Combine two genotypic data sets into one",
      "topics": [
        "hlaGenoCombine"
      ]
    },
    {
      "page": "hlaGenoLD",
      "title": "Composite Linkage Disequilibrium",
      "topics": [
        "hlaGenoLD"
      ]
    },
    {
      "page": "hlaGenoMFreq",
      "title": "Minor Allele Frequency",
      "topics": [
        "hlaGenoMFreq"
      ]
    },
    {
      "page": "hlaGenoMRate",
      "title": "Missing Rates Per SNP",
      "topics": [
        "hlaGenoMRate"
      ]
    },
    {
      "page": "hlaGenoMRate_Samp",
      "title": "Missing Rates Per Sample",
      "topics": [
        "hlaGenoMRate_Samp"
      ]
    },
    {
      "page": "hlaGenoSubset",
      "title": "Get a subset of genotypes",
      "topics": [
        "hlaGenoSubset"
      ]
    },
    {
      "page": "hlaGenoSwitchStrand",
      "title": "Allele flipping if needed",
      "topics": [
        "hlaGenoSwitchStrand"
      ]
    },
    {
      "page": "hlaLDMatrix",
      "title": "Composite Linkage Disequilibrium in a Region",
      "topics": [
        "hlaLDMatrix"
      ]
    },
    {
      "page": "hlaLociInfo",
      "title": "HLA/KIR Locus Information",
      "topics": [
        "hlaLociInfo"
      ]
    },
    {
      "page": "hlaMakeSNPGeno",
      "title": "Make a SNP genotype object",
      "topics": [
        "hlaMakeSNPGeno"
      ]
    },
    {
      "page": "hlaModelFiles",
      "title": "Load a model object from files",
      "topics": [
        "hlaModelFiles"
      ]
    },
    {
      "page": "hlaModelFromObj",
      "title": "Conversion between the in-memory model and the object that can be saved in a file",
      "topics": [
        "hlaModelFromObj",
        "hlaModelToObj"
      ]
    },
    {
      "page": "hlaOutOfBag",
      "title": "Out-of-bag estimation of overall accuracy, per-allele sensitivity, etc",
      "topics": [
        "hlaOutOfBag"
      ]
    },
    {
      "page": "hlaParallelAttrBagging",
      "title": "Build a HIBAG model via parallel computation",
      "topics": [
        "hlaParallelAttrBagging"
      ]
    },
    {
      "page": "hlaPredict",
      "title": "HIBAG model prediction (in parallel)",
      "topics": [
        "hlaPredict",
        "predict.hlaAttrBagClass"
      ]
    },
    {
      "page": "hlaPredMerge",
      "title": "Merge prediction results from multiple HIBAG models",
      "topics": [
        "hlaPredMerge"
      ]
    },
    {
      "page": "hlaPublish",
      "title": "Finalize a HIBAG model",
      "topics": [
        "hlaPublish"
      ]
    },
    {
      "page": "hlaReport",
      "title": "Format a report",
      "topics": [
        "hlaReport"
      ]
    },
    {
      "page": "hlaReportPlot",
      "title": "Format a report with figures",
      "topics": [
        "hlaReportPlot"
      ]
    },
    {
      "page": "hlaSampleAllele",
      "title": "Get sample IDs from HLA types with a filter",
      "topics": [
        "hlaSampleAllele"
      ]
    },
    {
      "page": "hlaSetKernelTarget",
      "title": "Set the CPU target",
      "topics": [
        "hlaSetKernelTarget"
      ]
    },
    {
      "page": "hlaSNPGenoClass",
      "title": "The class of SNP genotypes",
      "topics": [
        "hlaSNPGenoClass"
      ]
    },
    {
      "page": "hlaSNPID",
      "title": "Get SNP IDs and positions",
      "topics": [
        "hlaSNPID"
      ]
    },
    {
      "page": "hlaSplitAllele",
      "title": "Divide the samples randomly",
      "topics": [
        "hlaSplitAllele"
      ]
    },
    {
      "page": "hlaSubModelObj",
      "title": "Get a subset of individual classifiers",
      "topics": [
        "hlaSubModelObj"
      ]
    },
    {
      "page": "hlaUniqueAllele",
      "title": "Get unique HLA alleles",
      "topics": [
        "hlaUniqueAllele"
      ]
    },
    {
      "page": "plot.hlaAttrBagObj",
      "title": "Plot a HIBAG model",
      "topics": [
        "plot.hlaAttrBagClass",
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