{
  "_id": "6a489a65e06c18f0a6542d52",
  "Package": "HTGM3D",
  "Version": "1.0.3",
  "Date": "2026-04-26",
  "Title": "Three Dimensional High Throughput 'GoMiner'",
  "Authors@R": "c(\nperson(\"Barry\", \"Zeeberg\", email = \"barryz2013@gmail.com\",\nrole = c(\"aut\", \"cre\")))",
  "Maintainer": "Barry Zeeberg <barryz2013@gmail.com>",
  "Author": "Barry Zeeberg [aut, cre]",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "Description": "The Gene Ontology (GO) Consortium\n<https://geneontology.org/> organizes genes into hierarchical\ncategories based on biological process (BP), molecular function\n(MF) and cellular component (CC, i.e., subcellular\nlocalization). Tools such as 'GoMiner' (see Zeeberg, B.R.,\nFeng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>)\ncan leverage GO to perform ontological analysis of microarray\nand proteomics studies, typically generating a list of\nsignificant functional categories. To capture the benefit of\nall three ontologies, I developed 'HTGM3D', a three-dimensional\nversion of 'GoMiner'.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 05:14:54 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://barryzee.r-universe.dev",
  "Date/Publication": "2026-04-26 19:15:59 UTC",
  "RemoteUrl": "https://github.com/cran/HTGM3D",
  "RemoteRef": "HEAD",
  "RemoteSha": "fb7eab79fa61c3b366fd166442f835152d151027",
  "_user": "barryzee",
  "_type": "src",
  "_file": "HTGM3D_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/ae763c691d413f80b0b22f150138b10b8f0025d89f1ffed46cb9336078de6902",
  "_filesize": 2662168,
  "_sha256": "ae763c691d413f80b0b22f150138b10b8f0025d89f1ffed46cb9336078de6902",
  "_expires": "2026-10-12T05:30:11.000Z",
  "_created": "2026-07-04T05:14:54.000Z",
  "_published": "2026-07-04T05:30:13.411Z",
  "_jobs": [
    {
      "job": 85105391590,
      "time": 231,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8078607442"
    },
    {
      "job": 85105391621,
      "time": 225,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078606747"
    },
    {
      "job": 85105391592,
      "time": 107,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8078672620"
    },
    {
      "job": 85105391618,
      "time": 90,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078682682"
    },
    {
      "job": 85105132980,
      "time": 271,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078579284"
    },
    {
      "job": 85105391628,
      "time": 223,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8078606618"
    },
    {
      "job": 85105391617,
      "time": 143,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8078596880"
    },
    {
      "job": 85105391602,
      "time": 120,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8078594203"
    },
    {
      "job": 85105391593,
      "time": 151,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078597795"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411",
  "_status": "success",
  "_upstream": "https://github.com/cran/HTGM3D",
  "_commit": {
    "id": "fb7eab79fa61c3b366fd166442f835152d151027",
    "author": "Barry Zeeberg <barryz2013@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.3\n",
    "time": 1777230959
  },
  "_maintainer": {
    "name": "Barry Zeeberg",
    "email": "barryz2013@gmail.com",
    "login": "barryzee",
    "description": "",
    "uuid": 75148535
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "minimalistGODB",
      "role": "Imports"
    },
    {
      "package": "GoMiner",
      "role": "Imports"
    },
    {
      "package": "HTGM",
      "role": "Imports"
    },
    {
      "package": "HTGM2D",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "R2HTML",
      "role": "Imports"
    },
    {
      "package": "rgl",
      "role": "Imports"
    },
    {
      "package": "vprint",
      "role": "Imports"
    },
    {
      "package": "randomGODB",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "salesforcer",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-17",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0.1",
      "date": "2026-02-08"
    },
    {
      "name": "1.0.2",
      "date": "2026-02-20"
    },
    {
      "name": "1.0.3",
      "date": "2026-04-26"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "barryzee",
      "count": 4,
      "uuid": 75148535
    }
  ],
  "_userbio": {
    "uuid": 75148535,
    "type": "user",
    "name": "barryzee",
    "followers": 0
  },
  "_downloads": {
    "count": 472,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HTGM3D"
  },
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HTGM3D.html",
    "manual.pdf"
  ],
  "_realowner": "barryzee",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2025-05-30"
    },
    {
      "version": "1.0.1",
      "date": "2026-02-08"
    },
    {
      "version": "1.0.2",
      "date": "2026-02-20"
    },
    {
      "version": "1.0.3",
      "date": "2026-04-26"
    }
  ],
  "_exports": [
    "blackBodyRadiationColors",
    "catNum3",
    "graphIt",
    "HTGM3D",
    "HTGM3Ddriver",
    "insertCatSize",
    "interactWithGraph3D",
    "Jaccard3",
    "plot3Dmat",
    "pruneCatGenes",
    "showGenes",
    "subMatDiffs",
    "whichOS"
  ],
  "_datasets": [
    {
      "name": "cluster52",
      "title": "HTGM3D data set",
      "object": "cluster52",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Housekeeping_Genes",
      "title": "HTGM3D data set",
      "object": "Housekeeping_Genes",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Ensembl",
        "Gene.name",
        "Refseq",
        "CCDS.ID"
      ],
      "rows": 2833,
      "table": true,
      "tojson": true
    },
    {
      "name": "x_cg",
      "title": "HTGM3D data set",
      "object": "x_cg",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TGFB2",
        "TGFB1I1",
        "MYH9",
        "VCAN",
        "ADAM9",
        "DLC1",
        "FGF2",
        "CLIC4",
        "NEXN",
        "VCL",
        "IL6",
        "INHBA",
        "KCNMA1",
        "DBN1",
        "FEZ2",
        "ROBO3",
        "NOG",
        "SOCS5",
        "FOXO4",
        "SYNE1",
        "MT1X",
        "TRPC1",
        "SORD",
        "ACTB",
        "TNFRSF12A",
        "FERMT2",
        "DYNLL1",
        "MYL6",
        "SORBS3",
        "CHTS3",
        "DSE",
        "FOS",
        "JUN",
        "FGFR1",
        "FADS3",
        "MCAT",
        "OXSM",
        "GLRB",
        "PDGFC",
        "PVR",
        "DKK3",
        "TUFT1",
        "ACTN3",
        "ITGB1",
        "ALCAM",
        "CDH2",
        "CDH4",
        "ZYX"
      ],
      "rows": 12117,
      "table": true,
      "tojson": true
    },
    {
      "name": "x_l",
      "title": "HTGM3D data set",
      "object": "x_l",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "x_m11",
      "title": "HTGM3D data set",
      "object": "x_m11",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "x_mat",
      "title": "HTGM3D data set",
      "object": "x_mat",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "cat1",
        "cat2",
        "cat3",
        "lint",
        "n1",
        "n2",
        "n3",
        "hyperGenes"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    },
    {
      "name": "x_mat3d",
      "title": "HTGM3D data set",
      "object": "x_mat3d",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "cat1",
        "molecular_function",
        "cat2",
        "cellular_component",
        "cat3",
        "biological_process",
        "x",
        "y",
        "z",
        "xyz",
        "col",
        "lint",
        "n1",
        "n2",
        "n3",
        "hyperGenes"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "blackBodyRadiationColors",
      "title": "blackBodyRadiationColors",
      "topics": [
        "blackBodyRadiationColors"
      ]
    },
    {
      "page": "catNum3",
      "title": "catNum3",
      "topics": [
        "catNum3"
      ]
    },
    {
      "page": "cluster52",
      "title": "HTGM3D data set",
      "topics": [
        "cluster52"
      ]
    },
    {
      "page": "graphIt",
      "title": "graphIt",
      "topics": [
        "graphIt"
      ]
    },
    {
      "page": "Housekeeping_Genes",
      "title": "HTGM3D data set",
      "topics": [
        "Housekeeping_Genes"
      ]
    },
    {
      "page": "HTGM3D",
      "title": "HTGM3D",
      "topics": [
        "HTGM3D"
      ]
    },
    {
      "page": "HTGM3Ddriver",
      "title": "HTGM3Ddriver",
      "topics": [
        "HTGM3Ddriver"
      ]
    },
    {
      "page": "insertCatSize",
      "title": "insertCatSize",
      "topics": [
        "insertCatSize"
      ]
    },
    {
      "page": "interactWithGraph3D",
      "title": "interactWithGraph3D",
      "topics": [
        "interactWithGraph3D"
      ]
    },
    {
      "page": "Jaccard3",
      "title": "Jaccard3",
      "topics": [
        "Jaccard3"
      ]
    },
    {
      "page": "plot3Dmat",
      "title": "plot3Dmat",
      "topics": [
        "plot3Dmat"
      ]
    },
    {
      "page": "pruneCatGenes",
      "title": "pruneCatGenes",
      "topics": [
        "pruneCatGenes"
      ]
    },
    {
      "page": "showGenes",
      "title": "showGenes",
      "topics": [
        "showGenes"
      ]
    },
    {
      "page": "subMatDiffs",
      "title": "subMatDiffs",
      "topics": [
        "subMatDiffs"
      ]
    },
    {
      "page": "whichOS",
      "title": "whichOS",
      "topics": [
        "whichOS"
      ]
    },
    {
      "page": "x_cg",
      "title": "HTGM3D data set",
      "topics": [
        "x_cg"
      ]
    },
    {
      "page": "x_l",
      "title": "HTGM3D data set",
      "topics": [
        "x_l"
      ]
    },
    {
      "page": "x_m11",
      "title": "HTGM3D data set",
      "topics": [
        "x_m11"
      ]
    },
    {
      "page": "x_mat",
      "title": "HTGM3D data set",
      "topics": [
        "x_mat"
      ]
    },
    {
      "page": "x_mat3d",
      "title": "HTGM3D data set",
      "topics": [
        "x_mat3d"
      ]
    }
  ],
  "_rundeps": [
    "anytime",
    "askpass",
    "base64enc",
    "BH",
    "bit",
    "bit64",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "clipr",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "GoMiner",
    "gplots",
    "gtable",
    "gtools",
    "HGNChelper",
    "highr",
    "hms",
    "HTGM",
    "HTGM2D",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "isoband",
    "jaccard",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lifecycle",
    "lubridate",
    "magrittr",
    "memoise",
    "mime",
    "minimalistGODB",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "qvalue",
    "R2HTML",
    "R6",
    "randomGODB",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "reshape2",
    "rgl",
    "rlang",
    "rlist",
    "rmarkdown",
    "S7",
    "salesforcer",
    "sass",
    "scales",
    "shiny",
    "sourcetools",
    "splitstackshape",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyselect",
    "timechange",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vprint",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "yaml",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "HTGM3D.Rmd",
      "filename": "HTGM3D.html",
      "title": "Three Dimensional High Throughput GoMiner (HTGM3D)",
      "author": "Barry Zeeberg [aut, cre]",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-05-30 09:10:05",
      "modified": "2025-05-30 09:10:05",
      "commits": 1
    }
  ],
  "_score": 2.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "htgm3d",
  "_universes": [
    "barryzee"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-07-04T05:18:23.000Z",
      "distro": "resolute",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/4edce36df012efc6c39fc8f2159109a733249fcf83af0ed2f43f16cba238e315",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-07-04T05:18:23.000Z",
      "distro": "resolute",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/3667b5e95cf2c8027f65255fe03f78fa86a082f0cfbea0fd3315a76340b4eace",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-07-04T05:27:55.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/bd1c5758b647747561c0fdf2a1c8d4a9e6653f6df06ffbba2d6b91885d139164",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-07-04T05:29:31.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/1162742f6423be4c99cc0baefe449506b91abed9305dcb8f45faef4e4073cb99",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-07-04T05:19:00.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/771319131a1453971a25a79ba3459652a6fd08ebffdede7b0a6ceada209666ec",
      "status": "success",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-04T05:16:43.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/7d09f4cc400aa40b7f8bd74eaeee1fc76b64d7bdc55eaae1df3e3a1cd1753923",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-04T05:16:29.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/8fe2d9a5ef9ec97522509ca51758b33684b193609a85b1d8dd65ab11f2d488f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-07-04T05:16:45.000Z",
      "commit": "fb7eab79fa61c3b366fd166442f835152d151027",
      "fileid": "https://r2.ropensci.org/1d181ab652e9d38fcf60ac736071ff5324a73c0925569c47491cb8d312e1206f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28695836411"
    }
  ]
}