{ "_id": "6a478f5e8b9f0d9747cf0fd9", "Package": "HTGM4D", "Version": "1.0", "Date": "2026-04-29", "Title": "Four Dimensional High Throughput 'GoMiner'", "Authors@R": "c(\nperson(\"Barry\", \"Zeeberg\", email = \"barryz2013@gmail.com\",\nrole = c(\"aut\", \"cre\")))", "Maintainer": "Barry Zeeberg ", "Author": "Barry Zeeberg [aut, cre]", "LazyData": "true", "LazyDataCompression": "xz", "Description": "The Gene Ontology (GO) Consortium\n 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) )\ncan leverage GO to perform ontological analysis of microarray\nand proteomics studies, typically generating a list of\nsignificant functional categories. Microarray studies are\nusually analyzed with BP, whereas proteomics researchers often\nprefer CC. To capture the benefit of both of those ontologies,\nI now present an enhancement of the existing two-dimensional\nversion of 'High-Throughput GoMiner' ('HTGM2D'), which is\ncalled 'HTGM4D'. The original 'HTGM2D' is augmented by adding\ntwo instances of the original 'GoMiner' genes versus categories\nheatmaps, aligned with the categories axes of the 'HTGM2D'\nheatmap.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-02 08:12:26 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libssl-dev zlib1g-dev", "Repository": "https://barryzee.r-universe.dev", "Date/Publication": "2026-05-02 11:11:05 UTC", "RemoteUrl": "https://github.com/cran/HTGM4D", "RemoteRef": "HEAD", "RemoteSha": "1dbb0905003c967fca3017bca79bbca9f51a5962", "_user": "barryzee", "_type": "src", "_file": "HTGM4D_1.0.tar.gz", "_fileid": "https://r2.ropensci.org/351357ba1300279e17f7de1136dd0111bde51a09daa483e7b95c5a9a35c39a76", "_filesize": 3534070, "_sha256": "351357ba1300279e17f7de1136dd0111bde51a09daa483e7b95c5a9a35c39a76", "_expires": "2026-10-11T10:30:53.000Z", "_created": "2026-07-02T08:12:26.000Z", "_published": "2026-07-03T10:30:54.660Z", "_jobs": [ { "job": 84981100774, "time": 164, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8032797741" }, { "job": 84981101031, "time": 166, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8032798523" }, { "job": 84981101218, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8032777265" }, { "job": 84981100818, "time": 146, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8032790423" }, { "job": 84981100663, "time": 206, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8032734024" }, { "job": 84981101228, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8032797173" }, { "job": 84981101158, "time": 101, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8032774373" }, { "job": 84981101287, "time": 85, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8032768159" }, { "job": 84981101072, "time": 107, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8032776184" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432", "_status": "success", "_upstream": "https://github.com/cran/HTGM4D", "_commit": { "id": "1dbb0905003c967fca3017bca79bbca9f51a5962", "author": "Barry Zeeberg ", "committer": "cran-robot ", "message": "version 1.0\n", "time": 1777720265 }, "_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": "gplots", "role": "Imports" }, { "package": "vprint", "role": "Imports" }, { "package": "randomGODB", "role": "Imports" }, { "package": "HGNChelper", "role": "Imports" }, { "package": "png", "role": "Imports" }, { "package": "magick", "role": "Imports" }, { "package": "svglite", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "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": "2026-18", "n": 1 } ], "_tags": [ { "name": "1.0", "date": "2026-05-02" } ], "_stars": 0, "_contributors": [ { "user": "barryzee", "count": 1, "uuid": 75148535 } ], "_userbio": { "uuid": 75148535, "type": "user", "name": "barryzee", "followers": 0 }, "_downloads": { "count": 427, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HTGM4D" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HTGM4D.html", "manual.pdf" ], "_realowner": "barryzee", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2026-05-02" } ], "_exports": [ "buildSubdirs", "combine3SVG", "editor", "fillLines", "findSVGtags", "GoMiner4", "HTGM4D", "HTGM4Ddriver", "JaccardHeatMap4", "mergeGoMinerHTGM2D", "parseSVGline", "pngBorder", "pngDims", "pngDisplay3", "pngHeat", "renderSVG", "setSVGtransparency", "whoRanMe" ], "_datasets": [ { "name": "cluster52", "title": "HTGM4D data set", "object": "cluster52", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "x_jmat", "title": "HTGM4D data set", "object": "x_jmat", "class": [ "matrix", "array" ], "fields": [ "catr", "catc", "lint", "nr", "nc", "p" ], "rows": 36, "table": true, "tojson": true }, { "name": "x_l", "title": "HTGM4D data set", "object": "x_l", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "x_lines", "title": "HTGM4D data set", "object": "x_lines", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "x_svg1", "title": "HTGM4D data set", "object": "x_svg1", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "x_svg2", "title": "HTGM4D data set", "object": "x_svg2", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "x_svg3", "title": "HTGM4D data set", "object": "x_svg3", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "buildSubdirs", "title": "buildSubdirs", "topics": [ "buildSubdirs" ] }, { "page": "cluster52", "title": "HTGM4D data set", "topics": [ "cluster52" ] }, { "page": "combine3SVG", "title": "combine3SVG", "topics": [ "combine3SVG" ] }, { "page": "editor", "title": "editor", "topics": [ "editor" ] }, { "page": "fillLines", "title": "fillLines", "topics": [ "fillLines" ] }, { "page": "findSVGtags", "title": "findSVGtags", "topics": [ "findSVGtags" ] }, { "page": "GoMiner4", "title": "GoMiner4", "topics": [ "GoMiner4" ] }, { "page": "HTGM4D", "title": "HTGM4D", "topics": [ "HTGM4D" ] }, { "page": "HTGM4Ddriver", "title": "HTGM4Ddriver", "topics": [ "HTGM4Ddriver" ] }, { "page": "JaccardHeatMap4", "title": "JaccardHeatMap4", "topics": [ "JaccardHeatMap4" ] }, { "page": "mergeGoMinerHTGM2D", "title": "mergeGoMinerHTGM2D", "topics": [ "mergeGoMinerHTGM2D" ] }, { "page": "parseSVGline", "title": "parseSVGline", "topics": [ "parseSVGline" ] }, { "page": "pngBorder", "title": "pngBorder", "topics": [ "pngBorder" ] }, { "page": "pngDims", "title": "pngDims", "topics": [ "pngDims" ] }, { "page": "pngDisplay3", "title": "pngDisplay3", "topics": [ "pngDisplay3" ] }, { "page": "pngHeat", "title": "pngHeat", "topics": [ "pngHeat" ] }, { "page": "renderSVG", "title": "renderSVG", "topics": [ "renderSVG" ] }, { "page": "setSVGtransparency", "title": "setSVGtransparency", "topics": [ "setSVGtransparency" ] }, { "page": "whoRanMe", "title": "whoRanMe", "topics": [ "whoRanMe" ] }, { "page": "x_jmat", "title": "HTGM4D data set", "topics": [ "x_jmat" ] }, { "page": "x_l", "title": "HTGM4D data set", "topics": [ "x_l" ] }, { "page": "x_lines", "title": "HTGM4D data set", "topics": [ "x_lines" ] }, { "page": "x_svg1", "title": "HTGM4D data set", "topics": [ "x_svg1" ] }, { "page": "x_svg2", "title": "HTGM4D data set", "topics": [ "x_svg2" ] }, { "page": "x_svg3", "title": "HTGM4D data set", "topics": [ "x_svg3" ] } ], "_rundeps": [ "base64enc", "bitops", "bslib", "cachem", "caTools", "cli", "commonmark", "cpp11", "curl", "data.table", "digest", "farver", "fastmap", "fontawesome", "fs", "ggplot2", "glue", "GoMiner", "gplots", "gtable", "gtools", "HGNChelper", "HTGM", "HTGM2D", "htmltools", "httpuv", "isoband", "jaccard", "jquerylib", "jsonlite", "KernSmooth", "labeling", "later", "lifecycle", "magick", "magrittr", "memoise", "mime", "minimalistGODB", "otel", "plyr", "png", "promises", "qvalue", "R6", "randomGODB", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "sass", "scales", "shiny", "sourcetools", "splitstackshape", "stringi", "stringr", "svglite", "systemfonts", "textshaping", "vctrs", "viridisLite", "vprint", "withr", "xtable" ], "_vignettes": [ { "source": "HTGM4D.Rmd", "filename": "HTGM4D.html", "title": "Four Dimensional High Throughput GoMiner (HTGM4D)", "author": "Barry Zeeberg [aut, cre]", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-05-02 11:11:05", "modified": "2026-05-02 11:11:05", "commits": 1 } ], "_score": 2, "_indexed": true, "_nocasepkg": "htgm4d", "_universes": [ "barryzee" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0", "date": "2026-07-02T08:14:58.000Z", "distro": "resolute", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/ac66946e02c81426ab32bfe539b27455a7431dadac98f75585c85ec584e2c553", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.6.1", "os": "linux", "version": "1.0", "date": "2026-07-02T08:15:02.000Z", "distro": "resolute", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/a65d3791a20fb7f8cd7bca9d7183507943e4487df147561fcf4f7cc5a8ff9032", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-07-02T08:14:11.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/bdfb8841d5253e7a586c16dee6bb6d524975a4cd74369c0166fd3be43f841cf7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.6.1", "os": "mac", "version": "1.0", "date": "2026-07-02T08:14:36.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/7e3866ddfad728111cee5c32a20008af6c781281255685917bbe8b09eba7af68", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-07-02T08:15:26.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/0a740f3c0724c5fb379fcf18b420169c73c29ec5547f6eb373b8be2ba6831599", "status": "success", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-07-02T08:13:49.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/01cac9b857474b35fe246a7d6059365d7c720aeae64f4a16bbd634a4b40124cc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-07-02T08:13:37.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/6a67ddc27f5d3034a126b593316b3699b23e541074d90c4cbba24da4de966e76", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" }, { "r": "4.6.1", "os": "win", "version": "1.0", "date": "2026-07-02T08:13:56.000Z", "commit": "1dbb0905003c967fca3017bca79bbca9f51a5962", "fileid": "https://r2.ropensci.org/248be2089e3813aecac00abfdc7871ebca86aa3b49905de73bb771b062d710ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28575273432" } ] }