{ "_id": "6a1bed4f1d7bb097a0a20368", "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": "2026-05-31 06:56:45 UTC", "User": "root" }, "Author": "William Wheeler [aut, cre],\nDifei Wang [aut],\nIsaac Zhao [aut],\nYumi Jin [aut],\nCharles Rabkin [aut]", "Maintainer": "William Wheeler ", "MD5sum": "7cfb81f06d2e6b57d0f740465d4ace59", "_user": "bioc", "_type": "src", "_file": "GrafGen_1.9.0.tar.gz", "_fileid": "1e18dd4dc45d0597c3d1d0d6c622d11fec1e8991d3c80d8fa462d6cf31edfd96", "_filesize": 3128516, "_sha256": "1e18dd4dc45d0597c3d1d0d6c622d11fec1e8991d3c80d8fa462d6cf31edfd96", "_created": "2026-05-31T06:56:45.000Z", "_published": "2026-05-31T08:11:59.448Z", "_jobs": [ { "job": 78707052952, "time": 194, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314624662" }, { "job": 78707053007, "time": 202, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7314625686" }, { "job": 78707052978, "time": 336, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7314640449" }, { "job": 78707052976, "time": 218, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7314627717" }, { "job": 78707052979, "time": 244, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7314630804" }, { "job": 78707052985, "time": 123, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7315097399" }, { "job": 78707052986, "time": 331, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7314644321" }, { "job": 78707052999, "time": 131, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7315111547" }, { "job": 78707052983, "time": 453, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7314653304" }, { "job": 78706794923, "time": 306, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314604347" }, { "job": 78707052951, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314620204" }, { "job": 78707052982, "time": 196, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7314624962" }, { "job": 78707052993, "time": 254, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7314632018" }, { "job": 78707052984, "time": 189, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7314623942" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GrafGen", "_commit": { "id": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "author": "A Wokaty ", "committer": "A Wokaty ", "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": "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": 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", "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/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", "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": true, "_nocasepkg": "grafgen", "_universes": [ "bioc", "wheelerb" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-05-31T06:59:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "658932d70e17a068a4de925d4c14bd544cb9f84f9d2e09204360ad80494dcfbf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-05-31T07:01:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "100c842069abeda37ed967a06958a473a158e0fd95e28b3a84f04466caac26de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-05-31T06:59:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "3a90088a1ecd9c445c9e8519b00e70684840b9f32337d9b8bdc2eaab6bfba4c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-05-31T07:00:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "f0c04f6482c71c70a4f0f340684ef77b01276be8eee8e8758ccab6698a6e3471", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-05-31T08:08:47.000Z", "arch": "aarch64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "97c5ec50bcd21274e4c8f73dab3fa372cb6783b435010116c2e7866586fcee82", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-05-31T07:01:30.000Z", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "24743e6ba8b4d685d8d5678249ae3fa243a6e508ddbc1e6e8f3f1c2b40e25a92", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-05-31T08:10:47.000Z", "arch": "aarch64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "fd0debb61c68385aebabc559c26f2a5d6a1d319f965a0410838dc696b49fb3f7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-05-31T07:01:35.000Z", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "981d4ffb887dfb124995e2962f9b2a7fa990dee8af69bc757b918947037dba9b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-05-31T06:59:52.000Z", "arch": "emscripten", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "e47435fc5dec915b421b6331353ffec360a8052b2d19edb01e365bb2d39d9c84", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-05-31T06:58:38.000Z", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "294f012f0769cf8850df0aa51653fe4388280bbb054f7207161cb839668d4adb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-05-31T06:59:06.000Z", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "d474628e81557e2679301e23bb2741c48570e3284d3b8b96f9ed0af1c9461179", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" }, { "r": "4.6.0", "os": "win", "version": "1.9.0", "date": "2026-05-31T06:58:30.000Z", "arch": "x86_64", "commit": "12ab6340149b05f5d0170f2ac9050f37e7ec083a", "fileid": "d670a492e738f06c20dbb056d78fb8561f1c187fe4ce253dbd552fb4cf13413a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705816944" } ] }