{ "_id": "6a365b8c3efcd9bda440466a", "Package": "HTGM2D", "Version": "1.1.1", "Date": "2026-02-03", "Title": "Two 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 developed a two-dimensional version of 'High-Throughput\nGoMiner' ('HTGM2D'). I generate a 2D heat map whose axes are\nany two of BP, MF, or CC, and the value within a picture\nelement of the heat map reflects the Jaccard metric p-value for\nthe number of genes in common for the corresponding pair.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-20 09:17:51 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://barryzee.r-universe.dev", "Date/Publication": "2026-02-03 23:00:32 UTC", "RemoteUrl": "https://github.com/cran/HTGM2D", "RemoteRef": "HEAD", "RemoteSha": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "MD5sum": "973a6a90232b43f7e3ac1165fb8ce909", "_user": "barryzee", "_type": "src", "_file": "HTGM2D_1.1.1.tar.gz", "_fileid": "a94ea2e80ef773e61d7c26d97043767684ee2aa125862f9613f18b88b7a7b4e3", "_filesize": 1585753, "_sha256": "a94ea2e80ef773e61d7c26d97043767684ee2aa125862f9613f18b88b7a7b4e3", "_created": "2026-06-20T09:17:51.000Z", "_published": "2026-06-20T09:21:16.744Z", "_distro": "noble", "_jobs": [ { "job": 82472087787, "time": 132, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7764049630" }, { "job": 82472087788, "time": 166, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7764054253" }, { "job": 82472087816, "time": 111, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7764046900" }, { "job": 82472087815, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7764049390" }, { "job": 82471871066, "time": 209, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7764032816" }, { "job": 82472087783, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7764049045" }, { "job": 82472087814, "time": 99, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7764045439" }, { "job": 82472087818, "time": 78, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7764042849" }, { "job": 82472087819, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7764045471" } ], "_buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/HTGM2D", "_commit": { "id": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "author": "Barry Zeeberg ", "committer": "cran-robot ", "message": "version 1.1.1\n", "time": 1770159632 }, "_maintainer": { "name": "Barry Zeeberg", "email": "barryz2013@gmail.com", "login": "barryzee", "description": "", "uuid": 75148535 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "minimalistGODB", "role": "Imports" }, { "package": "GoMiner", "role": "Imports" }, { "package": "HTGM", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "jaccard", "role": "Imports" }, { "package": "vprint", "role": "Imports" }, { "package": "randomGODB", "role": "Imports" }, { "package": "HGNChelper", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2026-06", "n": 1 } ], "_tags": [ { "name": "1.1.1", "date": "2026-02-03" } ], "_stars": 0, "_contributors": [ { "user": "barryzee", "count": 3, "uuid": 75148535 } ], "_userbio": { "uuid": 75148535, "type": "user", "name": "barryzee", "followers": 0 }, "_downloads": { "count": 254, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HTGM2D" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HTGM2D.html", "manual.pdf" ], "_realowner": "barryzee", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2025-04-07" }, { "version": "1.1", "date": "2025-05-18" }, { "version": "1.1.1", "date": "2026-02-03" } ], "_exports": [ "catGenes", "compareGoMinerHTGM2D", "HTGM2D", "HTGM2Ddriver", "Jaccard", "JaccardHeatMap" ], "_datasets": [ { "name": "cluster52", "title": "HTGM2D data set", "object": "cluster52", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "GOGOA3small", "title": "HTGM2D data set", "object": "GOGOA3small", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Housekeeping_Genes", "title": "HTGM2D data set", "object": "Housekeeping_Genes", "class": [ "data.frame" ], "fields": [ "Ensembl", "Gene.name", "Refseq", "CCDS.ID" ], "rows": 2833, "table": true, "tojson": true }, { "name": "x_jmat", "title": "HTGM2D 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": "HTGM2D data set", "object": "x_l", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "x_m1", "title": "HTGM2D data set", "object": "x_m1", "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_m2", "title": "HTGM2D data set", "object": "x_m2", "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": 1832, "table": true, "tojson": true }, { "name": "x_mat", "title": "HTGM2D data set", "object": "x_mat", "class": [ "matrix", "array" ], "fields": [ "catr", "catc", "lint", "nr", "nc", "p" ], "rows": 35, "table": true, "tojson": true } ], "_help": [ { "page": "catGenes", "title": "catGenes", "topics": [ "catGenes" ] }, { "page": "cluster52", "title": "HTGM2D data set", "topics": [ "cluster52" ] }, { "page": "compareGoMinerHTGM2D", "title": "compareGoMinerHTGM2D", "topics": [ "compareGoMinerHTGM2D" ] }, { "page": "GOGOA3small", "title": "HTGM2D data set", "topics": [ "GOGOA3small" ] }, { "page": "Housekeeping_Genes", "title": "HTGM2D data set", "topics": [ "Housekeeping_Genes" ] }, { "page": "HTGM2D", "title": "HTGM2D", "topics": [ "HTGM2D" ] }, { "page": "HTGM2Ddriver", "title": "HTGM2Ddriver", "topics": [ "HTGM2Ddriver" ] }, { "page": "Jaccard", "title": "Jaccard", "topics": [ "Jaccard" ] }, { "page": "JaccardHeatMap", "title": "JaccardHeatMap", "topics": [ "JaccardHeatMap" ] }, { "page": "x_jmat", "title": "HTGM2D data set", "topics": [ "x_jmat" ] }, { "page": "x_l", "title": "HTGM2D data set", "topics": [ "x_l" ] }, { "page": "x_m1", "title": "HTGM2D data set", "topics": [ "x_m1" ] }, { "page": "x_m2", "title": "HTGM2D data set", "topics": [ "x_m2" ] }, { "page": "x_mat", "title": "HTGM2D data set", "topics": [ "x_mat" ] } ], "_rundeps": [ "base64enc", "bitops", "bslib", "cachem", "caTools", "cli", "commonmark", "cpp11", "data.table", "digest", "farver", "fastmap", "fontawesome", "fs", "ggplot2", "glue", "GoMiner", "gplots", "gtable", "gtools", "HGNChelper", "HTGM", "htmltools", "httpuv", "isoband", "jaccard", "jquerylib", "jsonlite", "KernSmooth", "labeling", "later", "lifecycle", "magrittr", "memoise", "mime", "minimalistGODB", "otel", "plyr", "promises", "qvalue", "R6", "randomGODB", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "sass", "scales", "shiny", "sourcetools", "splitstackshape", "stringi", "stringr", "vctrs", "viridisLite", "vprint", "withr", "xtable" ], "_vignettes": [ { "source": "HTGM2D.Rmd", "filename": "HTGM2D.html", "title": "Two Dimensional High Throughput GoMiner (HTGM2D)", "author": "Barry Zeeberg [aut, cre]", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-04-07 16:10:08", "modified": "2025-04-07 16:10:08", "commits": 1 } ], "_score": 2.778151250383644, "_indexed": true, "_nocasepkg": "htgm2d", "_universes": [ "barryzee" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-06-20T09:19:52.000Z", "distro": "noble", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "fe7129a25225c28b3b462be255cc865de6a4acd705a3f12ae969b80d62deb8e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.6.0", "os": "linux", "version": "1.1.1", "date": "2026-06-20T09:20:22.000Z", "distro": "noble", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "cef67902578ab60dbe85e0ea14ae12a5f8b4dca490685f367799793498538482", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-06-20T09:19:40.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "98107a43b8b7dc0288fc19a1ab7648a31d4c761d0616d21bf5799e930705e5d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.6.0", "os": "mac", "version": "1.1.1", "date": "2026-06-20T09:19:52.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "48da803548e7c8f59d90fbd26e0a8ed569e90a6c913db6da714f6785776ba045", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-06-20T09:20:18.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "4017b763d115915a782a949e4012fddbd50daddbf779c137e1361bf93f4a4b1e", "status": "success", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-06-20T09:19:11.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "b93ce12c4f009c2396d3a869859eb760ae2bcd6a6106b9f11d8abc5188bfcd18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-06-20T09:19:07.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "3348f607ce79ce017bb26fe8f9ea65cf301e9ae64051a68db2c680e3c6582315", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" }, { "r": "4.6.0", "os": "win", "version": "1.1.1", "date": "2026-06-20T09:19:21.000Z", "commit": "860e4a7b390e81039f2b10b3a1595858d4764e9a", "fileid": "611938cfb0dbd8b9e52bb1f14bbc02cc0d43ab45d043f085b0376b0fa7358528", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/27866686496" } ] }