{
  "_id": "6a22aaef0ef520ea2f58b5eb",
  "Package": "seqminer",
  "Type": "Package",
  "Title": "Efficiently Read Sequence Data (VCF Format, BCF Format, METAL\nFormat and BGEN Format) into R",
  "Version": "9.9",
  "Date": "2026-02-23",
  "Authors@R": "c(person(\"Xiaowei\", \"Zhan\", email = \"zhanxw@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Dajiang\", \"Liu\", email = \"dajiang.liu@gmail.com\", role = \"aut\"),\nperson(\"Attractive Chaos\", email = \"attractor@live.co.uk\", role = \"cph\", comment = \"We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.\"),\nperson(\"Broad Institute / Massachusetts Institute of Technology\", role = \"cph\"),\nperson(\"Genome Research Ltd (GRL)\", role = \"cph\"),\nperson(\"Facebook, Inc\", role = \"cph\"),\nperson(\"D. Richard Hipp\", role = \"cph\"))",
  "Maintainer": "Xiaowei Zhan <zhanxw@gmail.com>",
  "Description": "Integrate sequencing data (Variant call format, e.g. VCF\nor BCF) or meta-analysis results in R. This package can help\nyou (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g.\n1:100-200); (2) read 'RareMETAL' summary statistics files; (3)\nread tables from a 'tabix'-indexed files; (4) annotate VCF/BCF\nfiles; (5) create customized workflow based on Makefile.",
  "Copyright": "We have used the following software and made minimal\nnecessary changes: tabix, Heng Li <lh3@live.co.uk> (MIT\nlicense), SQLite (Public Domain), Zstandard (BSD license). For\ntabix, we removed standard IO related functions, e.g. printf,\nfprintf ; also changed its un-safe pointer arithmetics. For\nzstandard, we removed compiler (clang, MSVC) specific\npreprocessing flags.",
  "License": "GPL | file LICENSE",
  "URL": "http://zhanxw.github.io/seqminer/",
  "BugReports": "https://github.com/zhanxw/seqminer/issues",
  "Packaged": {
    "Date": "2026-06-05 10:49:53 UTC",
    "User": "root"
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  "SystemRequirements": "zlib headers and libraries, GNU make, optionally\nalso bzip2 and POSIX-compliant regex functions.",
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  "RoxygenNote": "7.2.3",
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  "Author": "Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos\n[cph] (We have used the following software and made minimal\nnecessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT\nlicense). We removed standard IO related functions, e.g.\nprintf, fprintf ; also changed its un-safe pointer\narithmetics.), Broad Institute / Massachusetts Institute of\nTechnology [cph], Genome Research Ltd (GRL) [cph], Facebook,\nInc [cph], D. Richard Hipp [cph]",
  "Config/pak/sysreqs": "make zlib1g-dev",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-02-24 09:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/seqminer",
  "RemoteRef": "HEAD",
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  "_published": "2026-06-05T10:54:39.179Z",
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  "_exports": [
    "addJob",
    "annotateGene",
    "annotatePlain",
    "annotateVcf",
    "createSingleChromosomeBCFIndex",
    "createSingleChromosomeVCFIndex",
    "download.annotation.resource",
    "getRefBase",
    "isInRange",
    "isTabixRange",
    "makeAnnotationParameter",
    "newJob",
    "newWorkflow",
    "openPlink",
    "readBGENToListByGene",
    "readBGENToListByRange",
    "readBGENToMatrixByGene",
    "readBGENToMatrixByRange",
    "readPlinkToMatrixByIndex",
    "readSingleChromosomeBCFToMatrixByRange",
    "readSingleChromosomeVCFToMatrixByRange",
    "readVCFToListByGene",
    "readVCFToListByRange",
    "readVCFToMatrixByGene",
    "readVCFToMatrixByRange",
    "rvmeta.readCovByRange",
    "rvmeta.readDataByGene",
    "rvmeta.readDataByRange",
    "rvmeta.readNullModel",
    "rvmeta.readScoreByRange",
    "rvmeta.readSkewByRange",
    "rvmeta.writeCovData",
    "rvmeta.writeScoreData",
    "tabix.createIndex",
    "tabix.createIndex.meta",
    "tabix.createIndex.vcf",
    "tabix.read",
    "tabix.read.header",
    "tabix.read.table",
    "validateAnnotationParameter",
    "writeWorkflow"
  ],
  "_help": [
    {
      "page": "sub-.PlinkFile",
      "title": "Read from binary PLINK file and return a genotype matrix",
      "topics": [
        "[.PlinkFile"
      ]
    },
    {
      "page": "addJob",
      "title": "Add a job to a workflow",
      "topics": [
        "addJob"
      ]
    },
    {
      "page": "annotateGene",
      "title": "Annotate a test variant",
      "topics": [
        "annotateGene"
      ]
    },
    {
      "page": "annotatePlain",
      "title": "Annotate a plain text file",
      "topics": [
        "annotatePlain"
      ]
    },
    {
      "page": "annotateVcf",
      "title": "Annotate a VCF file",
      "topics": [
        "annotateVcf"
      ]
    },
    {
      "page": "createSingleChromosomeBCFIndex",
      "title": "Create a single chromosome index",
      "topics": [
        "createSingleChromosomeBCFIndex"
      ]
    },
    {
      "page": "createSingleChromosomeVCFIndex",
      "title": "Create a single chromosome index",
      "topics": [
        "createSingleChromosomeVCFIndex"
      ]
    },
    {
      "page": "download.annotation.resource",
      "title": "Download annotation resources to a directory",
      "topics": [
        "download.annotation.resource"
      ]
    },
    {
      "page": "getCovPair",
      "title": "Extract pair of positions by ranges",
      "topics": [
        "getCovPair"
      ]
    },
    {
      "page": "getRefBase",
      "title": "Annotate a test variant",
      "topics": [
        "getRefBase"
      ]
    },
    {
      "page": "isDirWritable",
      "title": "Test whether directory is writable",
      "topics": [
        "isDirWritable"
      ]
    },
    {
      "page": "isInRange",
      "title": "Test whether a vector of positions are inside given ranges",
      "topics": [
        "isInRange"
      ]
    },
    {
      "page": "isTabixRange",
      "title": "Check if the inputs are valid tabix range such as chr1:2-300",
      "topics": [
        "isTabixRange"
      ]
    },
    {
      "page": "makeAnnotationParameter",
      "title": "Construct a usable set of annotation parameters",
      "topics": [
        "makeAnnotationParameter"
      ]
    },
    {
      "page": "newJob",
      "title": "Create a new job",
      "topics": [
        "newJob"
      ]
    },
    {
      "page": "newWorkflow",
      "title": "Create a new workflow",
      "topics": [
        "newWorkflow"
      ]
    },
    {
      "page": "openPlink",
      "title": "Open binary PLINK files",
      "topics": [
        "openPlink"
      ]
    },
    {
      "page": "readBGENToListByGene",
      "title": "Read information from BGEN file in a given range and return a list",
      "topics": [
        "readBGENToListByGene"
      ]
    },
    {
      "page": "readBGENToListByRange",
      "title": "Read information from BGEN file in a given range and return a list",
      "topics": [
        "readBGENToListByRange"
      ]
    },
    {
      "page": "readBGENToMatrixByGene",
      "title": "Read a gene from BGEN file and return a genotype matrix",
      "topics": [
        "readBGENToMatrixByGene"
      ]
    },
    {
      "page": "readBGENToMatrixByRange",
      "title": "Read a gene from BGEN file and return a genotype matrix",
      "topics": [
        "readBGENToMatrixByRange"
      ]
    },
    {
      "page": "readPlinkToMatrixByIndex",
      "title": "Read from binary PLINK file and return a genotype matrix",
      "topics": [
        "readPlinkToMatrixByIndex"
      ]
    },
    {
      "page": "readSingleChromosomeBCFToMatrixByRange",
      "title": "Read a range from BCF file and return a genotype matrix",
      "topics": [
        "readSingleChromosomeBCFToMatrixByRange"
      ]
    },
    {
      "page": "readSingleChromosomeVCFToMatrixByRange",
      "title": "Read a range from VCF file and return a genotype matrix",
      "topics": [
        "readSingleChromosomeVCFToMatrixByRange"
      ]
    },
    {
      "page": "readVCFToListByGene",
      "title": "Read information from VCF file in a given range and return a list",
      "topics": [
        "readVCFToListByGene"
      ]
    },
    {
      "page": "readVCFToListByRange",
      "title": "Read information from VCF file in a given range and return a list",
      "topics": [
        "readVCFToListByRange"
      ]
    },
    {
      "page": "readVCFToMatrixByGene",
      "title": "Read a gene from VCF file and return a genotype matrix",
      "topics": [
        "readVCFToMatrixByGene"
      ]
    },
    {
      "page": "readVCFToMatrixByRange",
      "title": "Read a gene from VCF file and return a genotype matrix",
      "topics": [
        "readVCFToMatrixByRange"
      ]
    },
    {
      "page": "rvmeta.readCovByRange",
      "title": "Read covariance by range from METAL-format files.",
      "topics": [
        "rvmeta.readCovByRange"
      ]
    },
    {
      "page": "rvmeta.readDataByGene",
      "title": "Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.",
      "topics": [
        "rvmeta.readDataByGene"
      ]
    },
    {
      "page": "rvmeta.readDataByRange",
      "title": "Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted.",
      "topics": [
        "rvmeta.readDataByRange"
      ]
    },
    {
      "page": "rvmeta.readNullModel",
      "title": "Read null model statistics",
      "topics": [
        "rvmeta.readNullModel"
      ]
    },
    {
      "page": "rvmeta.readScoreByRange",
      "title": "Read score test statistics by range from METAL-format files.",
      "topics": [
        "rvmeta.readScoreByRange"
      ]
    },
    {
      "page": "rvmeta.readSkewByRange",
      "title": "Read skew by range from METAL-format files.",
      "topics": [
        "rvmeta.readSkewByRange"
      ]
    },
    {
      "page": "rvmeta.writeCovData",
      "title": "Write covariance association statistics files.",
      "topics": [
        "rvmeta.writeCovData"
      ]
    },
    {
      "page": "rvmeta.writeScoreData",
      "title": "Write score-based association statistics files.",
      "topics": [
        "rvmeta.writeScoreData"
      ]
    },
    {
      "page": "SEQMINER",
      "title": "Efficiently Read Sequencing Data (VCF format, METAL format) into R",
      "topics": [
        "seqminer-package",
        "seqminer"
      ]
    },
    {
      "page": "tabix.createIndex",
      "title": "Create tabix index file, similar to running tabix in command line.",
      "topics": [
        "tabix.createIndex"
      ]
    },
    {
      "page": "tabix.createIndex.meta",
      "title": "Create tabix index for bgzipped MetaScore/MetaCov file",
      "topics": [
        "tabix.createIndex.meta"
      ]
    },
    {
      "page": "tabix.createIndex.vcf",
      "title": "Create tabix index for bgzipped VCF file",
      "topics": [
        "tabix.createIndex.vcf"
      ]
    },
    {
      "page": "tabix.read",
      "title": "Read tabix file, similar to running tabix in command line.",
      "topics": [
        "tabix.read"
      ]
    },
    {
      "page": "tabix.read.header",
      "title": "Read tabix file, similar to running tabix in command line.",
      "topics": [
        "tabix.read.header"
      ]
    },
    {
      "page": "tabix.read.table",
      "title": "Read tabix file, similar to running tabix in command line.",
      "topics": [
        "tabix.read.table"
      ]
    },
    {
      "page": "validateAnnotationParameter",
      "title": "Validate annotate parameter is valid",
      "topics": [
        "validateAnnotationParameter"
      ]
    },
    {
      "page": "verifyFilename",
      "title": "validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs",
      "topics": [
        "verifyFilename"
      ]
    },
    {
      "page": "writeWorkflow",
      "title": "Export workflow to Makefile",
      "topics": [
        "writeWorkflow"
      ]
    }
  ],
  "_readme": "https://github.com/cran/seqminer/raw/HEAD/README.md",
  "_rundeps": [],
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      "source": "bzip2",
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      "homepage": "https://sourceware.org/bzip2/",
      "description": "high-quality block-sorting file compressor library - runtime"
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      "shlib": "libzstd",
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      "name": "sqlite3",
      "homepage": "https://www.sqlite.org/",
      "description": "SQLite 3 shared library"
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  "_nocasepkg": "seqminer",
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  "_binaries": [
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