{
  "_id": "6a2be6ff3efcd9bda42cd912",
  "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": "7.3.2",
  "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]",
  "Packaged": {
    "Date": "2026-06-12 10:55:20 UTC",
    "User": "root"
  },
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-03-14 16:40:14 UTC",
  "RemoteUrl": "https://github.com/cran/rMVP",
  "RemoteRef": "HEAD",
  "RemoteSha": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
  "MD5sum": "b310b7dccd7a61f7d7350f4604bff19a",
  "_user": "cran",
  "_type": "src",
  "_file": "rMVP_1.4.6.tar.gz",
  "_fileid": "70c856fdc6d72991b677463fe11348acbdbff4af5ebea1b5ea184b62877f3243",
  "_filesize": 1064226,
  "_sha256": "70c856fdc6d72991b677463fe11348acbdbff4af5ebea1b5ea184b62877f3243",
  "_created": "2026-06-12T10:55:20.000Z",
  "_published": "2026-06-12T11:01:19.684Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81013144703,
      "time": 228,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7589763391"
    },
    {
      "job": 81013144678,
      "time": 168,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7589744586"
    },
    {
      "job": 81013144683,
      "time": 235,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7589765718"
    },
    {
      "job": 81013144669,
      "time": 189,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7589751476"
    },
    {
      "job": 81012516640,
      "time": 246,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7589691327"
    },
    {
      "job": 81013144623,
      "time": 156,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/27411151093",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/rMVP",
  "_commit": {
    "id": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
    "author": "Xiaolei Liu <xll198708@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.4.6\n",
    "time": 1773506414
  },
  "_maintainer": {
    "name": "Xiaolei Liu",
    "email": "xll198708@gmail.com",
    "login": "xll198708",
    "description": "",
    "uuid": 8975214
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "RcppProgress",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "bigmemory",
      "role": "LinkingTo"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "bigmemory",
      "role": "Imports"
    },
    {
      "package": "RhpcBLASctl",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2026-11",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.4.5",
      "date": "2025-07-23"
    },
    {
      "name": "1.4.6",
      "date": "2026-03-14"
    }
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "xiaoleiliubio",
      "count": 9,
      "uuid": 26868465
    },
    {
      "user": "xll198708",
      "count": 8,
      "uuid": 8975214
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 1267,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rMVP"
  },
  "_mentions": 12,
  "_devurl": "https://github.com/xiaolei-lab/rmvp",
  "_searchresults": 56,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/rMVP.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/xiaolei-lab/rmvp",
  "_realowner": "xiaolei-lab",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.99.15",
      "date": "2019-08-30"
    },
    {
      "version": "0.99.16",
      "date": "2019-09-24"
    },
    {
      "version": "0.99.17",
      "date": "2019-10-18"
    },
    {
      "version": "0.99.18",
      "date": "2020-03-19"
    },
    {
      "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"
    },
    {
      "version": "1.0.7",
      "date": "2023-09-01"
    },
    {
      "version": "1.0.8",
      "date": "2023-11-27"
    },
    {
      "version": "1.1.1",
      "date": "2024-08-31"
    },
    {
      "version": "1.3.0",
      "date": "2024-12-17"
    },
    {
      "version": "1.3.5",
      "date": "2025-01-10"
    },
    {
      "version": "1.4.0",
      "date": "2025-01-22"
    },
    {
      "version": "1.4.5",
      "date": "2025-07-23"
    },
    {
      "version": "1.4.6",
      "date": "2026-03-14"
    }
  ],
  "_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": "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"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "bigmemory",
    "bigmemory.sri",
    "MASS",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "RhpcBLASctl",
    "uuid"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "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"
    },
    {
      "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"
    }
  ],
  "_score": 3.151994637553623,
  "_indexed": false,
  "_nocasepkg": "rmvp",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://xiaolei-lab.r-universe.dev/rMVP",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.6",
      "date": "2026-06-12T10:59:07.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
      "fileid": "6428b88c47a933b7db576b53f07b8892e6838c8f7d7a53bc149b2982eb25217b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27411151093"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.6",
      "date": "2026-06-12T10:58:11.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
      "fileid": "4e26e512fe208d770f381d8fd687e3fd9b6ea0d119f6cf3dd948c5b706b9a3f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27411151093"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4.6",
      "date": "2026-06-12T10:59:11.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
      "fileid": "a8e3280c81ef39231cb706bed417a45c28a21385210ba4e1f9167225b09ee520",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27411151093"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4.6",
      "date": "2026-06-12T10:58:28.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "92fe146c00f73ee6e5de488a47d5eadbf0aed2ed",
      "fileid": "43257626f8dc0d4ac6da23e0ae197a9aacd03ab25c64d382c82f7dade4bb0647",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/27411151093"
    }
  ]
}