{
  "_id": "6a1950ffacfb0bcc41ddf8c1",
  "Package": "parati",
  "Type": "Package",
  "Title": "Parental Allele Transmission Inference for Trio Genotype Data",
  "Version": "1.0.0",
  "Authors@R": "person(\"Jinyi\", \"Che\", email = \"chejinyi777@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Infers maternal and paternal transmitted and\nnon-transmitted alleles from phased trio genotype data. The\npackage supports SNP-level analyses of genetic nurture and\ntransgenerational effects. It interoperates with Bioconductor\nVCF infrastructure through support for VariantAnnotation::VCF\nobjects and returns R objects for downstream analysis.",
  "URL": "https://github.com/newche/parati",
  "BugReports": "https://github.com/newche/parati/issues",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "biocViews": "Genetics, SNP, Sequencing, VariantAnnotation, Software",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:57 UTC",
  "RemoteUrl": "https://github.com/bioc/parati",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 07:32:00 UTC",
    "User": "root"
  },
  "Author": "Jinyi Che [aut, cre]",
  "Maintainer": "Jinyi Che <chejinyi777@gmail.com>",
  "MD5sum": "032ce7001e55deb981a3d2c4623810d7",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "parati_1.0.0.tar.gz",
  "_fileid": "ee498d9c19da2f0766c36b9ab9ec74c2abe1d67d6313ca8dd23d5fac1a2dd4f1",
  "_filesize": 1958949,
  "_sha256": "ee498d9c19da2f0766c36b9ab9ec74c2abe1d67d6313ca8dd23d5fac1a2dd4f1",
  "_created": "2026-05-29T07:32:00.000Z",
  "_published": "2026-05-29T08:40:31.827Z",
  "_jobs": [
    {
      "job": 78457731282,
      "time": 181,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285513859"
    },
    {
      "job": 78457731263,
      "time": 294,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7285546547"
    },
    {
      "job": 78457731248,
      "time": 325,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285555233"
    },
    {
      "job": 78457731284,
      "time": 197,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7286630086"
    },
    {
      "job": 78457731281,
      "time": 205,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286631009"
    },
    {
      "job": 78457035433,
      "time": 298,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285461544"
    },
    {
      "job": 78457731243,
      "time": 158,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285507895"
    },
    {
      "job": 78457731288,
      "time": 274,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7285540418"
    },
    {
      "job": 78457731280,
      "time": 269,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7285539647"
    },
    {
      "job": 78457731247,
      "time": 273,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7285540612"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/parati",
  "_commit": {
    "id": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381617
  },
  "_maintainer": {
    "name": "Jinyi Che",
    "email": "chejinyi777@gmail.com"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "vcfR",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "optparse",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "waldo",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-05",
      "n": 3
    },
    {
      "week": "2026-09",
      "n": 8
    },
    {
      "week": "2026-13",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "snp",
    "sequencing",
    "variantannotation",
    "software"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "newche",
      "count": 9,
      "uuid": 93996868
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 232,
    "source": "https://www.bioconductor.org/packages/stats/bioc/parati"
  },
  "_devurl": "https://github.com/newche/parati",
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/parati.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "haplotype_infer",
    "parati_run",
    "read_vcf_by_chr",
    "vcf_dt_to_vcfR",
    "write_vcf_dt",
    "write_vcf_obj"
  ],
  "_help": [
    {
      "page": "haplotype_infer",
      "title": "Infer parental transmitted and non-transmitted alleles",
      "topics": [
        "haplotype_infer"
      ]
    },
    {
      "page": "parati_run",
      "title": "Run PARATI inference workflow",
      "topics": [
        "parati_run"
      ]
    },
    {
      "page": "read_vcf_by_chr",
      "title": "Read VCF by chromosome",
      "topics": [
        "read_vcf_by_chr"
      ]
    },
    {
      "page": "vcf_dt_to_vcfR",
      "title": "Convert data.table to vcfR object",
      "topics": [
        "vcf_dt_to_vcfR"
      ]
    },
    {
      "page": "write_vcf_dt",
      "title": "Write VCF data.table to file",
      "topics": [
        "write_vcf_dt"
      ]
    },
    {
      "page": "write_vcf_obj",
      "title": "Write vcfR object to file",
      "topics": [
        "write_vcf_obj"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/parati/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "ape",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "digest",
    "dplyr",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "memuse",
    "mgcv",
    "mime",
    "nlme",
    "openssl",
    "openxlsx",
    "permute",
    "pillar",
    "pinfsc50",
    "pkgconfig",
    "png",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "Rcpp",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vcfR",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "parati-workflow.Rmd",
      "filename": "parati-workflow.html",
      "title": "PARATI: Parental Allele Transmission Inference",
      "author": "Jinyi Che",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Introduction",
        "Installation",
        "Load packages and example data",
        "Run PARATI from a VCF file path",
        "Explore returned results",
        "Export result files",
        "Output files and summary columns",
        "Meaning of sim_perc_summary columns",
        "Integration with Bioconductor VCF workflows",
        "Inputs",
        "1. Trio genotype VCF",
        "2. Family index table",
        "Notes",
        "Session Info"
      ],
      "created": "2026-01-30 18:20:28",
      "modified": "2026-04-14 17:21:56",
      "commits": 4
    }
  ],
  "_score": 4.3979400086720375,
  "_indexed": false,
  "_nocasepkg": "parati",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/parati",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T07:35:00.000Z",
      "distro": "noble",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "5217e63a90bcf9a555ec382560282a03ae2f733f0648a4ced93ec830bbc16536",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T07:35:34.000Z",
      "distro": "noble",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "8e1504efce70df8a35a8a0c1cb5acc37ad968b3ad6bc8cbefd90162c3871b4be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T08:38:24.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "0f4dca9318b194c87295ac4aaf5eb196d12c8592288db18dc1b8a79595bca2dc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T08:38:28.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "4cd0303c1a3eae1f7ab9b713b1d1cade1e9e1b78814cbe0d61955ca74791bd76",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-05-29T07:34:56.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "007b4a88c4d87cd7d6ce39a4c4da68d61113925be6e6d6fc0412b15f53d0f8dc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T07:33:59.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "03adfe9972d91a42cceb2b3af17f270bff6d15108fc8dabc1768d26e270b1ba3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T07:34:00.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "deba82b0156574752b77d149b3307d5b12ef3db66c9010b6581d917b64bae5ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T07:33:51.000Z",
      "commit": "4abcfd9e58da699b8609e6e9910ebc22d5b602ca",
      "fileid": "6c826b2113fb3c327fbd37237097cbcb7f929285d4a3bdd07c9e2029e5e7cebd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624223292"
    }
  ]
}