{ "_id": "6aca7ffffe5cc25786e8a572", "Package": "BG2", "Type": "Package", "Title": "Performs Bayesian GWAS analysis for non-Gaussian data using BG2", "Version": "1.12.0", "Authors@R": "c(person(given = \"Jacob\",\nfamily = \"Williams\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jwilliams@vt.edu\",\ncomment = c(ORCID = \"0000-0002-6425-1365\")),\nperson(given = \"Shuangshuang\",\nfamily = \"Xu\",\nrole = \"aut\"),\nperson(given = \"Marco\",\nfamily = \"Ferreira\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-4705-5661\")))", "Description": "This package is built to perform GWAS analysis for\nnon-Gaussian data using BG2. The BG2 method uses penalized\nquasi-likelihood along with nonlocal priors in a two step\nmanner to identify SNPs in GWAS analysis. The research related\nto this package was supported in part by National Science\nFoundation awards DMS 1853549 and DMS 2054173.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "biocViews": "Bayesian, AssayDomain, SNP, GenomeWideAssociation", "RoxygenNote": "7.2.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:59:35 UTC", "RemoteUrl": "https://github.com/bioc/BG2", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 16:45:27 UTC", "User": "root" }, "Author": "Jacob Williams [aut, cre] (ORCID:\n),\nShuangshuang Xu [aut],\nMarco Ferreira [aut] (ORCID: )", "Maintainer": "Jacob Williams ", "_user": "bioc-release", "_type": "src", "_file": "BG2_1.12.0.tar.gz", "_fileid": "https://r2.ropensci.org/8dacbf2766f0dfde5e31a9d82c2b8f8d8884eaa89191dba775921008f71a4a11", "_filesize": 1068145, "_sha256": "8dacbf2766f0dfde5e31a9d82c2b8f8d8884eaa89191dba775921008f71a4a11", "_expires": "2027-01-18T18:12:13.000Z", "_created": "2026-10-10T16:45:27.000Z", "_published": "2026-10-10T18:12:14.998Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_upstream": "https://github.com/bioc/BG2", "_commit": { "id": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381175 }, "_maintainer": { "name": "Jacob Williams", "email": "jwilliams@vt.edu", "login": "willja16", "description": "", "uuid": 60931617, "orcid": "0000-0002-6425-1365" }, "_distro": "resolute", "_jobs": [ { "job": 114262301697, "time": 146, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11676416666" }, { "job": 114262301695, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11675723665" }, { "job": 114262301699, "time": 283, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11675529001" }, { "job": 114262301718, "time": 397, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11678352672" }, { "job": 114262301987, "time": 375, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11677973128" }, { "job": 114261278886, "time": 314, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11676217745" }, { "job": 114262301706, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11675583618" }, { "job": 114262301764, "time": 401, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11675334842" }, { "job": 114262301693, "time": 248, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11676211987" }, { "job": 114262301765, "time": 435, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11675997448" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "GA", "version": ">= 3.2", "role": "Imports" }, { "package": "caret", "version": ">= 6.0-86", "role": "Imports" }, { "package": "memoise", "version": ">= 1.1.0", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.2-18", "role": "Imports" }, { "package": "MASS", "version": ">= 7.3-58.1", "role": "Imports" }, { "package": "stats", "version": ">= 4.2.2", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "formatR", "role": "Suggests" }, { "package": "rrBLUP", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.13.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.12.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "bayesian", "assaydomain", "snp", "genomewideassociation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 272, "source": "https://www.bioconductor.org/packages/stats/bioc/BG2" }, "_searchresults": 3, "_rbuild": "4.6.1", "_assets": [ "extra/BG2.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "BG2" ], "_datasets": [ { "name": "kinship", "title": "A. Thaliana Kinship matrix", "object": "kinship", "file": "kinship.rda", "class": [ "matrix", "array" ], "fields": [], "rows": 328, "table": true, "tojson": true }, { "name": "SNPs", "title": "A. Thaliana Genotype matrix", "object": "SNPs", "file": "SNPs.rda", "class": [ "matrix", "array" ], "fields": [], "rows": 328, "table": true, "tojson": true }, { "name": "Y_binary", "title": "A. Thaliana Simulated Phenotype matrix", "object": "Y_binary", "file": "Y_binary.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "Y_poisson", "title": "A. Thaliana Simulated Phenotype matrix", "object": "Y_poisson", "file": "Y_poisson.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "BG2", "title": "Performs BG2 as described in the manuscript, Xu, Williams, and Ferreira BG2: Bayesian variable selection in generalized linear mixed models with non-local priors for non-Gaussian GWAS data, Bioinformatics, Submitted.", "topics": [ "BG2" ] }, { "page": "kinship", "title": "A. Thaliana Kinship matrix", "topics": [ "kinship" ] }, { "page": "SNPs", "title": "A. Thaliana Genotype matrix", "topics": [ "SNPs" ] }, { "page": "Y_binary", "title": "A. Thaliana Simulated Phenotype matrix", "topics": [ "Y_binary" ] }, { "page": "Y_poisson", "title": "A. Thaliana Simulated Phenotype matrix", "topics": [ "Y_poisson" ] } ], "_readme": "https://github.com/bioc/BG2/raw/RELEASE_3_23/README.md", "_rundeps": [ "cachem", "caret", "class", "cli", "clock", "codetools", "cpp11", "crayon", "data.table", "diagram", "digest", "dplyr", "e1071", "farver", "fastmap", "foreach", "future", "future.apply", "GA", "generics", "ggplot2", "globals", "glue", "gower", "gtable", "hardhat", "ipred", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "memoise", "ModelMetrics", "nlme", "nnet", "numDeriv", "parallelly", "pillar", "pkgconfig", "plyr", "pROC", "prodlim", "progressr", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "recipes", "reshape2", "rlang", "rpart", "S7", "scales", "shape", "sparsevctrs", "SQUAREM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tzdb", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "BG2.Rmd", "filename": "BG2.html", "title": "BG2", "author": "Shuangshuang Xu, Jacob Williams, and Marco A.R. Ferreira", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Functions", "Model/Model Assumptions", "Examples", "Simulated Data", "BG2 Poisson Example", "BG2 Binary Example", "References" ], "created": "2022-12-12 13:11:14", "modified": "2023-01-08 18:07:22", "commits": 8 } ], "_score": 4, "_indexed": false, "_nocasepkg": "bg2", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/BG2", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.12.0", "date": "2026-10-10T16:48:27.000Z", "distro": "resolute", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/a54ff5255abc722c313e7fcd23d49aae4a06105251b6bb8d2d0a1574d02f5f1d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.6.1", "os": "linux", "version": "1.12.0", "date": "2026-10-10T16:49:18.000Z", "distro": "resolute", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/032a23c7b84d43ac8c512d0bf7d4f34912b522d43731b0ad9ca6de824f0420a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.5.3", "os": "mac", "version": "1.12.0", "date": "2026-10-10T18:06:35.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/5e3ef2743f743c156a69218825450f4151806041fd07b3efd289fb6a2cc15476", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.6.1", "os": "mac", "version": "1.12.0", "date": "2026-10-10T18:06:48.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/1ad66003ea300531255c8b8c9bfaa4eff6a0756f6e8b6d41cd03b1b11b34f103", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.6.0", "os": "wasm", "version": "1.12.0", "date": "2026-10-10T16:47:50.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/03f1ba4541687dcb5cb7ccf80bcbcd8378254691ba59fa691c02145016c8b174", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.7.0", "os": "win", "version": "1.12.0", "date": "2026-10-10T16:46:47.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/d5fd7725ac8b3a5ba7092da454d038fab59fecefa51d35bd25dbc25b4de1091b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.5.3", "os": "win", "version": "1.12.0", "date": "2026-10-10T16:46:32.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/aad66c90a42365be29bdd28e8f34c47227ea4ebea3966b720b89ac832e224010", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" }, { "r": "4.6.1", "os": "win", "version": "1.12.0", "date": "2026-10-10T16:47:24.000Z", "commit": "e45b59b28376c92f61f5aa2fd6f9aa7b6d3486c5", "fileid": "https://r2.ropensci.org/f09492e7fb4fc2c4410db51269d9b912a3af4243664263d52e63b6be1ff53ae5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38068590146" } ] }