{
  "_id": "6a1adf171d7bb097a09ec047",
  "Package": "GrafGen",
  "Title": "Classification of Helicobacter Pylori Genomes",
  "Version": "1.8.0",
  "Date": "2024-12-16",
  "Authors@R": "c(person(given=\"William\", family=\"Wheeler\", role=c(\"aut\", \"cre\"),\nemail=\"wheelerb@imsweb.com\"),\nperson(given=\"Difei\", family=\"Wang\", role=\"aut\",\nemail=\"difei.wang2@nih.gov\"),\nperson(given=\"Isaac\", family=\"Zhao\", role=\"aut\"),\nperson(given=\"Yumi\", family=\"Jin\", role=\"aut\"),\nperson(given=\"Charles\", family=\"Rabkin\", role=\"aut\",\nemail=\"rabkinc@exchange.nih.gov\"))",
  "Description": "To classify Helicobacter pylori genomes according to\ngenetic distance from nine reference populations. The nine\nreference populations are hpgpAfrica, hpgpAfrica-distant,\nhpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope,\nhpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex\npopulations are Africa, Europe and Asia.",
  "License": "GPL-2",
  "biocViews": "Genetics, Software, GenomeAnnotation, Classification",
  "NeedsCompilation": "yes",
  "BugReports": "https://github.com/wheelerb/GrafGen/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:37 UTC",
  "RemoteUrl": "https://github.com/bioc/GrafGen",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
  "Packaged": {
    "Date": "2026-05-30 09:15:02 UTC",
    "User": "root"
  },
  "Author": "William Wheeler [aut, cre],\nDifei Wang [aut],\nIsaac Zhao [aut],\nYumi Jin [aut],\nCharles Rabkin [aut]",
  "Maintainer": "William Wheeler <wheelerb@imsweb.com>",
  "MD5sum": "2944ca6a7656a7fde44cabbc8a31f42c",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "GrafGen_1.8.0.tar.gz",
  "_fileid": "977cbb62053052c96d2935a35978cd36e1890fd871eeda80c556f1e9c51d15cc",
  "_filesize": 3128549,
  "_sha256": "977cbb62053052c96d2935a35978cd36e1890fd871eeda80c556f1e9c51d15cc",
  "_created": "2026-05-30T09:15:02.000Z",
  "_published": "2026-05-30T12:59:02.967Z",
  "_jobs": [
    {
      "job": 78639020363,
      "time": 176,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307157949"
    },
    {
      "job": 78639020398,
      "time": 227,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307127345"
    },
    {
      "job": 78639020402,
      "time": 249,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307165145"
    },
    {
      "job": 78639020397,
      "time": 202,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307125062"
    },
    {
      "job": 78639020387,
      "time": 283,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307168486"
    },
    {
      "job": 78639020401,
      "time": 139,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308352305"
    },
    {
      "job": 78639020382,
      "time": 258,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307149116"
    },
    {
      "job": 78639020370,
      "time": 123,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308350969"
    },
    {
      "job": 78639020391,
      "time": 252,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307147863"
    },
    {
      "job": 78638649687,
      "time": 280,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307105061"
    },
    {
      "job": 78639020365,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307155976"
    },
    {
      "job": 78639020371,
      "time": 201,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307160127"
    },
    {
      "job": 78639020372,
      "time": 179,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307158442"
    },
    {
      "job": 78639020375,
      "time": 178,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307158144"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GrafGen",
  "_commit": {
    "id": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
    "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": 1777381357
  },
  "_maintainer": {
    "name": "William Wheeler",
    "email": "wheelerb@imsweb.com",
    "login": "wheelerb",
    "description": "",
    "uuid": 33498685
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "software",
    "genomeannotation",
    "classification",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "wheelerb",
      "count": 59,
      "uuid": 33498685
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 255,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GrafGen"
  },
  "_devurl": "https://github.com/wheelerb/grafgen",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GrafGen.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wheelerb/grafgen",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "createApp",
    "grafGen",
    "grafGenPlot",
    "interactivePlot",
    "interactiveReferencePlot"
  ],
  "_datasets": [
    {
      "name": "example_metadata",
      "title": "Metadata for examples",
      "object": "example_metadata",
      "file": "example_metadata.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Country.code",
        "Country"
      ],
      "rows": 206,
      "table": true,
      "tojson": true
    },
    {
      "name": "grafGen_example_results",
      "title": "Example results",
      "object": "grafGen_example_results",
      "file": "grafGen_example_results.rda",
      "class": [
        "grafpop"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "grafGen_reference_dataframe",
      "title": "Reference data results for plots",
      "object": "grafGen_reference_dataframe",
      "file": "grafGen_reference_dataframe.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample",
        "GD1_x",
        "GD2_y",
        "GD3_z",
        "E_percent",
        "F_percent",
        "A_percent",
        "hpgpEurope",
        "hpgpAfrica",
        "hpgpAsia",
        "hpgpAfroamerica",
        "hpgpEuroamerica",
        "hpgpMediterranea",
        "hpgpEurasia",
        "hpgpAklavik86-like",
        "hpgpAfrica-distant",
        "Refpop",
        "Nearest_neighbor",
        "Separation_percent",
        "Country.code",
        "Country"
      ],
      "rows": 1011,
      "table": true,
      "tojson": true
    },
    {
      "name": "grafGen_reference_results",
      "title": "Reference data results",
      "object": "grafGen_reference_results",
      "file": "grafGen_reference_results.rda",
      "class": [
        "grafpop"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HpyloriData",
      "title": "H. pylori data",
      "object": "HpyloriData",
      "file": "HpyloriData.rda",
      "class": [
        "UnstitchedGPos"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "GrafGen-package",
      "title": "Classify H. pylori genomes",
      "topics": [
        "GrafGen-package",
        "GrafGen"
      ]
    },
    {
      "page": "createApp",
      "title": "R Shiny App",
      "topics": [
        "createApp"
      ]
    },
    {
      "page": "example_metadata",
      "title": "Metadata for examples",
      "topics": [
        "example_metadata"
      ]
    },
    {
      "page": "grafGen",
      "title": "Reference population for H. pylori strains",
      "topics": [
        "grafGen"
      ]
    },
    {
      "page": "grafGen_example_results",
      "title": "Example results",
      "topics": [
        "grafGen_example_results"
      ]
    },
    {
      "page": "grafGen_reference_dataframe",
      "title": "Reference data results for plots",
      "topics": [
        "grafGen_reference_dataframe"
      ]
    },
    {
      "page": "grafGen_reference_results",
      "title": "Reference data results",
      "topics": [
        "grafGen_reference_results"
      ]
    },
    {
      "page": "grafGenPlot",
      "title": "Plot results",
      "topics": [
        "grafGenPlot"
      ]
    },
    {
      "page": "HpyloriData",
      "title": "H. pylori data",
      "topics": [
        "HpyloriData"
      ]
    },
    {
      "page": "interactivePlot",
      "title": "Interactive plot of user's data",
      "topics": [
        "interactivePlot"
      ]
    },
    {
      "page": "interactiveReferencePlot",
      "title": "Interactive plot of the reference data",
      "topics": [
        "interactiveReferencePlot"
      ]
    },
    {
      "page": "s3",
      "title": "Plot and Print",
      "topics": [
        "plot.grafpop",
        "print.grafpop"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GrafGen/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "backports",
    "base64enc",
    "BiocGenerics",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "cli",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plotly",
    "polynom",
    "promises",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rmarkdown",
    "rstatix",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "sourcetools",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "zoo"
  ],
  "_sysdeps": [
    {
      "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"
    }
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "GrafGen: Classifying Subpopulations of H. pylori Genomes",
      "author": "William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin and Charles Rabkin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing the GrafGen package from Bioconductor",
        "Loading the package",
        "Example data",
        "Running grafGen()",
        "Interactive plots",
        "R shiny app",
        "Session Information"
      ],
      "created": "2024-01-17 16:05:50",
      "modified": "2024-02-28 21:44:11",
      "commits": 2
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": false,
  "_nocasepkg": "grafgen",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/GrafGen",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T09:18:16.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "b6c8cc7e1bd900cc9ffa9d465cd7af7ff9f15f00b19b5f4db7c95873a71214c3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T09:24:47.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "a49022b79c2001c0adb40d412937277f638192e3b1d5ee49578163e37f0ff528",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T09:17:56.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "e87207aba8bea8c48929ed0bd0e74f2546198c7c97dc7b0e67b17b67191f3125",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.8.0",
      "date": "2026-05-30T09:25:18.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "04a399aaf01c4feb777baad593cde2aba9d49a3db3979bbeb59045229bc81d4b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T12:57:49.000Z",
      "arch": "aarch64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "5d9528188f3baccc2d3df0943296fa7a245fc89645aade44bf7c3b033587a9ad",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T09:21:27.000Z",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "a8ab9026cae9369bdaafb1f0daf6b38b0fb8090f7325ae73f60f53903a5772dd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T12:57:35.000Z",
      "arch": "aarch64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "1fe53a0376335df2dfd7f346f52f2c3cb27f7ac9934f7f9df1900f667d070d26",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.8.0",
      "date": "2026-05-30T09:21:22.000Z",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "6f01de93e7bcf269821359e56c9e54ec1b881bdcbd6d96f0b0ed74b40bc84e8f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.8.0",
      "date": "2026-05-30T09:24:24.000Z",
      "arch": "emscripten",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "f7f4e65081d82cbed8e131139abbbec9365a2da7a25cc4c26357f5c0e86cc821",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T09:23:09.000Z",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "4fd065f06b14301cd4f23c70d84341effdefa0a95178c7c5f818921a4183561e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T09:23:16.000Z",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "3a3d41dd618801b966ae3f6b4345b22d5183c76410e85f5df1a174d0a14d6dab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.8.0",
      "date": "2026-05-30T09:23:04.000Z",
      "arch": "x86_64",
      "commit": "2680b1d32bce7b88920e0c2c2366ea53599521cd",
      "fileid": "6c4a39134dd845adf991538026fae5025508edc5c3c74e920c2c10ba9561cb1b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625128563"
    }
  ]
}