{
  "_id": "6a645c59059529545f576791",
  "Package": "GrafGen",
  "Title": "Classification of Helicobacter Pylori Genomes",
  "Version": "1.9.0",
  "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.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:37 UTC",
  "RemoteUrl": "https://github.com/bioc/GrafGen",
  "RemoteRef": "HEAD",
  "RemoteSha": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
  "Packaged": {
    "Date": "2026-07-25 06:42:17 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>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GrafGen_1.9.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/06ccf19a2f64467149df9d3321bb7ff95aa24a2e471631e3d971df15e661dedc",
  "_filesize": 3129325,
  "_sha256": "06ccf19a2f64467149df9d3321bb7ff95aa24a2e471631e3d971df15e661dedc",
  "_expires": "2026-11-02T06:48:50.000Z",
  "_created": "2026-07-25T06:42:17.000Z",
  "_published": "2026-07-25T06:48:57.621Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 7
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240",
  "_status": "success",
  "_upstream": "https://github.com/bioc/GrafGen",
  "_commit": {
    "id": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381357
  },
  "_maintainer": {
    "name": "William Wheeler",
    "email": "wheelerb@imsweb.com",
    "login": "wheelerb",
    "description": "",
    "uuid": 33498685
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 89653317268,
      "time": 205,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8616685070"
    },
    {
      "job": 89653317287,
      "time": 226,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8616688446"
    },
    {
      "job": 89653317281,
      "time": 321,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8616704766"
    },
    {
      "job": 89653317314,
      "time": 233,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8616689799"
    },
    {
      "job": 89653317275,
      "time": 332,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8616706772"
    },
    {
      "job": 89653317316,
      "time": 156,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8616680481"
    },
    {
      "job": 89653317321,
      "time": 254,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8616697002"
    },
    {
      "job": 89653317303,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8616686485"
    },
    {
      "job": 89653317301,
      "time": 310,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8616704717"
    },
    {
      "job": 89652900854,
      "time": 326,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8616649122"
    },
    {
      "job": 89653317276,
      "time": 175,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8616679604"
    },
    {
      "job": 89653317269,
      "time": 197,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8616683578"
    },
    {
      "job": 89653317299,
      "time": 209,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8616686162"
    },
    {
      "job": 89653317280,
      "time": 203,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8616684624"
    }
  ],
  "_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": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_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",
    "followers": 451,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 258,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GrafGen"
  },
  "_devurl": "https://github.com/wheelerb/grafgen",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_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/HEAD/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",
    "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": "16-20260322-1ubuntu1",
      "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": true,
  "_nocasepkg": "grafgen",
  "_universes": [
    "bioc",
    "wheelerb"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-25T06:45:33.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/deac940df1b369801ff4fefb496e1098af0ed793b2cd2c58e0f8c18e7c04fe06",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-25T06:46:44.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/88b9f91dcbafa740beda32450d6cb771db37b71f235b29d54c2f8952cff19bf5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-25T06:45:41.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/95b7ec3047341f7d28dfa3e2324031a2db72ee6249396f4171fcfe71591cefba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-25T06:46:59.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/e713facea8193def4410e58acee93e991cfa7aeb83efda5b8c1385325f669f6c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-25T06:44:49.000Z",
      "arch": "aarch64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/3799c5c754199f98265c962fb67f727fe49da8f3db28af999231728a7cc7eb07",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-25T06:45:41.000Z",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/1334b5d2ff8ed8afd3fd5ce95a2cb38d56063bb1b124d0cec723f9576c0c1e23",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-25T06:44:51.000Z",
      "arch": "aarch64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/c80828b246be5d0fceb283634d24b511cda462d2da5ee28480a29dd30b870a6e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-25T06:46:03.000Z",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/2607b8b31c49cd7243f5fd3a1cf3725fb9358c9dd5564cd2bba92f0e20bb8631",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-07-25T06:45:35.000Z",
      "arch": "emscripten",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/7a39869470231d159bb69ae83e54afa32d5ba447b86a5d6f1d2ec7b9247a2ada",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-25T06:44:01.000Z",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/c3d181d8646580b9c6ded5a83c3a9e99d4ff1275866de0afd283087c04e9ffb1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-25T06:44:21.000Z",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/7d6916c4bf3fe3953c81917826cf3a5b8e977de23b8096652e64caa36ee5e3ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-25T06:44:16.000Z",
      "arch": "x86_64",
      "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a",
      "fileid": "https://r2.ropensci.org/6fe184027adc3aa17f9a3f62d7fa2308ee808b5c2fd8a2590d01d302997ec5af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/30147813240"
    }
  ]
}