{
  "_id": "6a170b43acfb0bcc41d93300",
  "Package": "rMVP",
  "Type": "Package",
  "Title": "Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS\nTool",
  "Version": "1.4.6",
  "Date": "2026-03-10",
  "Authors@R": "c( person(\"Lilin\", \"Yin\", role = \"aut\"), \nperson(\"Haohao\", \"Zhang\", role = \"aut\"),\nperson(\"Zhenshuang\", \"Tang\", role = \"aut\"),\nperson(\"Jingya\", \"Xu\", role = \"aut\"),\nperson(\"Dong\", \"Yin\", role = \"aut\"),\nperson(\"Zhiwu\", \"Zhang\", role = \"aut\"),\nperson(\"Xiaohui\", \"Yuan\", role = \"aut\"),\nperson(\"Mengjin\", \"Zhu\", role = \"aut\"),\nperson(\"Shuhong\", \"Zhao\", role = \"aut\"),\nperson(\"Xinyun\", \"Li\", role = \"aut\"),\nperson(\"Qishan\", \"Wang\", role = \"ctb\"),\nperson(\"Feng\", \"Tian\", role = \"ctb\"),\nperson(\"Hyunmin\", \"Kang\", role = \"ctb\"),\nperson(\"Xiang\", \"Zhou\", role = \"ctb\"),\nperson(\"Xiaolei\", \"Liu\", role = c(\"cre\", \"aut\", \"cph\"), email = \"xll198708@gmail.com\"))",
  "Description": "A memory-efficient, visualize-enhanced,\nparallel-accelerated Genome-Wide Association Study (GWAS) tool.\nIt can (1) effectively process large data, (2) rapidly evaluate\npopulation structure, (3) efficiently estimate variance\ncomponents several algorithms, (4) implement\nparallel-accelerated association tests of markers three\nmethods, (5) globally efficient design on GWAS process\ncomputing, (6) enhance visualization of related information.\n'rMVP' contains three models GLM (Alkes Price (2006)\n<DOI:10.1038/ng1847>), MLM (Jianming Yu (2006)\n<DOI:10.1038/ng1702>) and FarmCPU (Xiaolei Liu (2016)\n<doi:10.1371/journal.pgen.1005767>); variance components\nestimation methods EMMAX (Hyunmin Kang (2008)\n<DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph\nLippert (2011) <DOI:10.1038/nmeth.1681>, R implementation from\n'GAPIT2': You Tang and Xiaolei Liu (2016)\n<DOI:10.1371/journal.pone.0107684> and 'SUPER': Qishan Wang and\nFeng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE\nregression (Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).",
  "License": "Apache License 2.0",
  "Encoding": "UTF-8",
  "URL": "https://github.com/xiaolei-lab/rMVP",
  "BugReports": "https://github.com/xiaolei-lab/rMVP/issues",
  "NeedsCompilation": "yes",
  "RoxygenNote": "7.3.3",
  "Maintainer": "Xiaolei Liu <xll198708@gmail.com>",
  "Author": "Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [aut],\nJingya Xu [aut], Dong Yin [aut], Zhiwu Zhang [aut], Xiaohui\nYuan [aut], Mengjin Zhu [aut], Shuhong Zhao [aut], Xinyun Li\n[aut], Qishan Wang [ctb], Feng Tian [ctb], Hyunmin Kang [ctb],\nXiang Zhou [ctb], Xiaolei Liu [cre, aut, cph]",
  "Repository": "https://xiaolei-lab.r-universe.dev",
  "Date/Publication": "2026-05-27 12:31:58 UTC",
  "RemoteUrl": "https://github.com/xiaolei-lab/rmvp",
  "RemoteRef": "HEAD",
  "RemoteSha": "78fc9e636439c3b5171ee05d0460e3ad4df3129a",
  "Packaged": {
    "Date": "2026-05-27 15:11:38 UTC",
    "User": "root"
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  "MD5sum": "6d5a6dc13e8bae0920fc31a4fbc28782",
  "_user": "xiaolei-lab",
  "_type": "src",
  "_file": "rMVP_1.4.6.tar.gz",
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  "_created": "2026-05-27T15:11:38.000Z",
  "_published": "2026-05-27T15:18:27.148Z",
  "_distro": "noble",
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    "author": "Zankrut Goyani <68992386+zankrut20@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "refactor: production-grade code quality pass — dedup, vectorize, C++17, RAII, safety (#117)\n\nrefactor: production-grade code quality pass — dedup, vectorize, C++17, RAII, safety",
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  "_devurl": "https://github.com/xiaolei-lab/rmvp",
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  "_topics": [
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_realowner": "xiaolei-lab",
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      "date": "2019-08-30"
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    {
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      "date": "2019-10-18"
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    {
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      "date": "2020-03-19"
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    {
      "version": "1.0.0",
      "date": "2020-05-07"
    },
    {
      "version": "1.0.3",
      "date": "2020-07-17"
    },
    {
      "version": "1.0.4",
      "date": "2020-09-01"
    },
    {
      "version": "1.0.5",
      "date": "2021-03-02"
    },
    {
      "version": "1.0.6",
      "date": "2021-04-18"
    },
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      "version": "1.0.7",
      "date": "2023-09-01"
    },
    {
      "version": "1.0.8",
      "date": "2023-11-27"
    },
    {
      "version": "1.1.1",
      "date": "2024-08-31"
    },
    {
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      "date": "2024-12-17"
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      "version": "1.3.5",
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      "version": "1.4.0",
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      "date": "2025-07-23"
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  "_exports": [
    "as.big.matrix",
    "attach.big.matrix",
    "deepcopy",
    "is.big.matrix",
    "MVP",
    "MVP.BRENT.Vg.Ve",
    "MVP.Data",
    "MVP.Data.Bfile2MVP",
    "MVP.Data.Hapmap2MVP",
    "MVP.Data.impute",
    "MVP.Data.Kin",
    "MVP.Data.Map",
    "MVP.Data.MVP2Bfile",
    "MVP.Data.Numeric2MVP",
    "MVP.Data.PC",
    "MVP.Data.Pheno",
    "MVP.Data.VCF2MVP",
    "MVP.EMMA.Vg.Ve",
    "MVP.FarmCPU",
    "MVP.FaSTLMM.LL",
    "MVP.GLM",
    "MVP.HE.Vg.Ve",
    "MVP.Hist",
    "MVP.K.VanRaden",
    "MVP.MLM",
    "MVP.PCA",
    "MVP.PCAplot",
    "MVP.Report",
    "MVP.Report.Density",
    "MVP.Report.QQplot",
    "MVP.Version",
    "new"
  ],
  "_datasets": [
    {
      "name": "pig60K",
      "title": "Genotyped by pig 60k chip",
      "object": "pig60K",
      "file": "pig60K.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SNP",
        "Chromosome",
        "Position",
        "trait1",
        "trait2",
        "trait3"
      ],
      "rows": 44580,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-farmcpu_specify",
      "title": "To get indicator (TURE or FALSE) for GI based on GP",
      "topics": [
        ".farmcpu_specify"
      ]
    },
    {
      "page": "dot-farmcpu_sub",
      "title": ".farmcpu_sub",
      "topics": [
        ".farmcpu_sub"
      ]
    },
    {
      "page": "FarmCPU.FaSTLMM.LL",
      "title": "FarmCPU.FaSTLMM.LL Evaluation of the maximum likelihood using FaST-LMM method Last update: January 11, 2017 Requirement: pheno, snp.pool, and X0 must have same taxa order. Requirement: No missing data",
      "topics": [
        "FarmCPU.FaSTLMM.LL"
      ]
    },
    {
      "page": "MVP",
      "title": "MVP, Memory-efficient, Visualization-enhanced, Parallel-accelerated",
      "topics": [
        "MVP"
      ]
    },
    {
      "page": "MVP.BRENT.Vg.Ve",
      "title": "MVP.BRENT.Vg.Ve variance component estimation using the BRENT method",
      "topics": [
        "MVP.BRENT.Vg.Ve"
      ]
    },
    {
      "page": "MVP.Data",
      "title": "MVP.Data: To prepare data for MVP package",
      "topics": [
        "MVP.Data"
      ]
    },
    {
      "page": "MVP.Data.Bfile2MVP",
      "title": "MVP.Data.Bfile2MVP: To transform plink binary data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.Bfile2MVP"
      ]
    },
    {
      "page": "MVP.Data.Hapmap2MVP",
      "title": "MVP.Data.Hapmap2MVP: To transform Hapmap data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.Hapmap2MVP"
      ]
    },
    {
      "page": "MVP.Data.impute",
      "title": "MVP.Data.impute: To impute the missing genotype Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.impute"
      ]
    },
    {
      "page": "MVP.Data.Kin",
      "title": "Kinship",
      "topics": [
        "MVP.Data.Kin"
      ]
    },
    {
      "page": "MVP.Data.Map",
      "title": "MVP.Data.Map: To check map file Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.Map"
      ]
    },
    {
      "page": "MVP.Data.MVP2Bfile",
      "title": "MVP.Data.MVP2Bfile: To transform MVP data to binary format Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.MVP2Bfile"
      ]
    },
    {
      "page": "MVP.Data.Numeric2MVP",
      "title": "MVP.Data.Numeric2MVP: To transform Numeric data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.Numeric2MVP"
      ]
    },
    {
      "page": "MVP.Data.PC",
      "title": "Principal component analysis",
      "topics": [
        "MVP.Data.PC"
      ]
    },
    {
      "page": "MVP.Data.Pheno",
      "title": "MVP.Data.Pheno: To clean up phenotype file Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.Pheno"
      ]
    },
    {
      "page": "MVP.Data.VCF2MVP",
      "title": "MVP.Data.VCF2MVP: To transform vcf data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018",
      "topics": [
        "MVP.Data.VCF2MVP"
      ]
    },
    {
      "page": "MVP.EMMA.Vg.Ve",
      "title": "Estimate variance components using EMMA",
      "topics": [
        "MVP.EMMA.Vg.Ve"
      ]
    },
    {
      "page": "MVP.FarmCPU",
      "title": "Perform GWAS using FarmCPU method",
      "topics": [
        "MVP.FarmCPU"
      ]
    },
    {
      "page": "MVP.FaSTLMM.LL",
      "title": "Evaluation of the maximum likelihood using FaST-LMM method",
      "topics": [
        "MVP.FaSTLMM.LL"
      ]
    },
    {
      "page": "MVP.GLM",
      "title": "To perform GWAS with GLM and MLM model and get the P value of SNPs",
      "topics": [
        "MVP.GLM"
      ]
    },
    {
      "page": "MVP.HE.Vg.Ve",
      "title": "To estimate variance component using HE regression",
      "topics": [
        "MVP.HE.Vg.Ve"
      ]
    },
    {
      "page": "MVP.Hist",
      "title": "Phenotype distribution histogram",
      "topics": [
        "MVP.Hist"
      ]
    },
    {
      "page": "MVP.K.VanRaden",
      "title": "Calculate Kinship matrix by VanRaden method",
      "topics": [
        "MVP.K.VanRaden"
      ]
    },
    {
      "page": "MVP.MLM",
      "title": "To perform GWAS with GLM and MLM model and get the P value of SNPs",
      "topics": [
        "MVP.MLM"
      ]
    },
    {
      "page": "MVP.PCA",
      "title": "Principal Component Analysis",
      "topics": [
        "MVP.PCA"
      ]
    },
    {
      "page": "MVP.PCAplot",
      "title": "PCA Plot",
      "topics": [
        "MVP.PCAplot"
      ]
    },
    {
      "page": "MVP.Report",
      "title": "MVP.Report",
      "topics": [
        "MVP.Report"
      ]
    },
    {
      "page": "MVP.Report.Density",
      "title": "SNP Density",
      "topics": [
        "MVP.Report.Density"
      ]
    },
    {
      "page": "MVP.Report.QQplot",
      "title": "QQ Plot",
      "topics": [
        "MVP.Report.QQplot"
      ]
    },
    {
      "page": "MVP.Version",
      "title": "Print MVP Banner",
      "topics": [
        "MVP.Version"
      ]
    },
    {
      "page": "pig60K",
      "title": "Genotyped by pig 60k chip",
      "topics": [
        "pig60K"
      ]
    }
  ],
  "_readme": "https://github.com/xiaolei-lab/rmvp/raw/HEAD/README.md",
  "_rundeps": [
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    "bigmemory",
    "bigmemory.sri",
    "MASS",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "RhpcBLASctl",
    "uuid"
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  "_sysdeps": [
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      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
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    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
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  "_score": 8.3172120356328,
  "_indexed": true,
  "_nocasepkg": "rmvp",
  "_universes": [
    "xiaolei-lab",
    "xll198708"
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