{ "_id": "6a1ace301d7bb097a09dfb33", "Package": "GGPA", "Type": "Package", "Title": "graph-GPA: A graphical model for prioritizing GWAS results and\ninvestigating pleiotropic architecture", "Version": "1.25.0", "Date": "2020-02-25", "Author": "Dongjun Chung, Hang J. Kim, Carter Allen", "Maintainer": "Dongjun Chung ", "Description": "Genome-wide association studies (GWAS) is a widely used\ntool for identification of genetic variants associated with\nphenotypes and diseases, though complex diseases featuring many\ngenetic variants with small effects present difficulties for\ntraditional these studies. By leveraging pleiotropy, the\nstatistical power of a single GWAS can be increased. This\npackage provides functions for fitting graph-GPA, a statistical\nframework to prioritize GWAS results by integrating pleiotropy.\n'GGPA' package provides user-friendly interface to fit\ngraph-GPA models, implement association mapping, and generate a\nphenotype graph.", "License": "GPL (>= 2)", "URL": "https://github.com/dongjunchung/GGPA/", "RcppModules": "cGGPAmodule", "NeedsCompilation": "yes", "biocViews": "Software, StatisticalMethod, Classification,\nGenomeWideAssociation, SNP, Genetics, Clustering,\nMultipleComparison, Preprocessing, GeneExpression,\nDifferentialExpression", "SystemRequirements": "GNU make", "Config/pak/sysreqs": "make libicu-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:28 UTC", "RemoteUrl": "https://github.com/bioc/GGPA", "RemoteRef": "HEAD", "RemoteSha": "9f0cd1156668de0c5a36dadf10232423332c720c", "Packaged": { "Date": "2026-05-30 08:11:42 UTC", "User": "root" }, "MD5sum": "a8b622f06aff9670c793e3012dcf99e9", "_user": "bioc", "_type": "src", "_file": "GGPA_1.25.0.tar.gz", "_fileid": "329db1822f077082bae3e3a96da26f1b269629be1c186dcc98e0ac2e106326e5", "_filesize": 4916389, "_sha256": "329db1822f077082bae3e3a96da26f1b269629be1c186dcc98e0ac2e106326e5", "_created": "2026-05-30T08:11:42.000Z", "_published": "2026-05-30T11:46:56.549Z", "_jobs": [ { "job": 78635767610, "time": 167, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306750449" }, { "job": 78635767653, "time": 256, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306759142" }, { "job": 78635767624, "time": 317, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306764858" }, { "job": 78635767660, "time": 248, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306758280" }, { "job": 78635767646, "time": 315, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306764719" }, { "job": 78635767693, "time": 183, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307941441" }, { "job": 78635767712, "time": 350, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7306769171" }, { "job": 78635767721, "time": 218, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307944554" }, { "job": 78635767698, "time": 319, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306765495" }, { "job": 78635561719, "time": 240, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306734558" }, { "job": 78635767649, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306747227" }, { "job": 78635767702, "time": 327, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306765788" }, { "job": 78635767615, "time": 360, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306768892" }, { "job": 78635767613, "time": 337, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306766644" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GGPA", "_commit": { "id": "9f0cd1156668de0c5a36dadf10232423332c720c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380748 }, "_maintainer": { "name": "Dongjun Chung", "email": "dongjun.chung@gmail.com", "login": "dongjunchung", "description": "", "uuid": 6115175 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "GGally", "role": "Depends" }, { "package": "network", "role": "Depends" }, { "package": "sna", "role": "Depends" }, { "package": "scales", "role": "Depends" }, { "package": "matrixStats", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.11.3", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "software", "statisticalmethod", "classification", "genomewideassociation", "snp", "genetics", "clustering", "multiplecomparison", "preprocessing", "geneexpression", "differentialexpression", "openblas", "cpp" ], "_stars": 1, "_contributors": [ { "user": "dongjunchung", "count": 20, "uuid": 6115175 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 321, "source": "https://www.bioconductor.org/packages/stats/bioc/GGPA" }, "_devurl": "https://github.com/dongjunchung/ggpa", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GGPA.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/dongjunchung/ggpa", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assoc", "estimates", "fdr", "GGPA", "plot", "show" ], "_datasets": [ { "name": "simulation", "title": "Simulation dataa for graph-GPA", "object": "simulation", "file": "simulation.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "GGPA-package", "title": "graph-GPA", "topics": [ "GGPA-package" ] }, { "page": "assoc", "title": "Association mapping", "topics": [ "assoc", "assoc,GGPA-method" ] }, { "page": "GGPA", "title": "Fit graph-GPA model", "topics": [ "GGPA" ] }, { "page": "GGPA-class", "title": "Class \"GGPA\"", "topics": [ "estimates", "estimates,GGPA-method", "fdr", "fdr,GGPA-method", "GGPA-class", "plot,GGPA,missing-method", "plot,GGPA-method", "show,GGPA-method" ] }, { "page": "simulation", "title": "Simulation dataa for graph-GPA", "topics": [ "simulation" ] } ], "_readme": "https://github.com/bioc/GGPA/raw/HEAD/README.md", "_rundeps": [ "cli", "coda", "cpp11", "crayon", "dplyr", "farver", "forcats", "generics", "GGally", "ggplot2", "ggstats", "glue", "gtable", "hms", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "network", "patchwork", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "sna", "statnet.common", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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": "GGPA-example.Rnw", "filename": "GGPA-example.pdf", "title": "GGPA", "engine": "utils::Sweave", "headings": [], "created": "2020-02-25 15:44:37", "modified": "2020-04-12 17:16:02", "commits": 5 } ], "_score": 4, "_indexed": true, "_nocasepkg": "ggpa", "_universes": [ "bioc", "dongjunchung" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:14:33.000Z", "distro": "noble", "arch": "aarch64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "50e0dc61819729969fd825e03e8df0a1e747400a90253cbd1baa2f5cd47cbb50", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:15:06.000Z", "distro": "noble", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "2eb6ce19b56090dfddee7464d2ac8ddc4a1ed38104a03e06a6c4a08ff3b4786f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:14:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "2017b667693b33746dec214e7f6b75d82ec6af82296a9b77e13eb7863130dce6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:15:03.000Z", "distro": "noble", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "ce753c23bf2913e2ec9690772235303035e3af4302d04a0d5caf0ee299de7e6b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T11:44:21.000Z", "arch": "aarch64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "1d7afd7cc5d87b0d12ff273ed8ac762c13e84670c02339fc70321a6e24f72333", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T08:15:17.000Z", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "70c65f49f707287546cefa4f43ff5498026b18a99d9101332579da569b112450", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T11:44:29.000Z", "arch": "aarch64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "a60007a58c9aa6ac10c2401c5f1162f50fd36041dd89b5f485712c540fd47b30", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T08:14:59.000Z", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "56446b389d0ec131e7b0f40b2a2847be92f8f0ee58216e15bc3932bea19611b8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T08:14:15.000Z", "arch": "emscripten", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "69f000957d7dcb3f2a811f1146fb657f3ac6077436a0b9b3f63196bad3c587c1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:13:56.000Z", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "cdbc1b36851101fd018ca242dec0074e9f474cce703f63e35e42c82c5ebad761", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:13:29.000Z", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "33590da2f5ae80436a833ba870778934f5e6b542648e40dfe8e237ed45ccdd09", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:13:23.000Z", "arch": "x86_64", "commit": "9f0cd1156668de0c5a36dadf10232423332c720c", "fileid": "ddbf52d0d4cf1f508464168bc046a02df09b44f4d339b4b011bcbdefad6365b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678849999" } ] }