{ "_id": "6abe3d3599f7aa8c6aa542f8", "Package": "gcatest", "Title": "Genotype Conditional Association TEST", "Version": "2.13.0", "Authors@R": "c(\nperson(given = \"Wei\",\nfamily = \"Hao\",\nrole = \"aut\",\nemail = \"whao@princeton.edu\"),\nperson(given = \"Minsun\",\nfamily = \"Song\",\nrole = \"aut\"),\nperson(given = \"Alejandro\",\nfamily = \"Ochoa\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alejandro.ochoa@duke.edu\",\ncomment = c(ORCID = \"0000-0003-4928-3403\")),\nperson(given = \"John D.\",\nfamily = \"Storey\",\nrole = \"aut\",\nemail = \"jstorey@princeton.edu\",\ncomment = c(ORCID = \"0000-0001-5992-402X\"))\n)", "Encoding": "UTF-8", "LazyData": "true", "Description": "GCAT is an association test for genome wide association\nstudies that controls for population structure under a general\nclass of trait models. This test conditions on the trait,\nwhich makes it immune to confounding by unmodeled environmental\nfactors. Population structure is modeled via logistic factors,\nwhich are estimated using the `lfa` package.", "VignetteBuilder": "knitr", "License": "GPL (>= 3)", "biocViews": "SNP, DimensionReduction, PrincipalComponent,\nGenomeWideAssociation", "BugReports": "https://github.com/StoreyLab/gcatest/issues", "URL": "https://github.com/StoreyLab/gcatest", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libx11-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:59 UTC", "RemoteUrl": "https://github.com/bioc/gcatest", "RemoteRef": "HEAD", "RemoteSha": "d5181b61f07044840f96242b66a4560f6447136e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-01 10:55:11 UTC", "User": "root" }, "Author": "Wei Hao [aut],\nMinsun Song [aut],\nAlejandro Ochoa [aut, cre] (ORCID:\n),\nJohn D. Storey [aut] (ORCID: )", "Maintainer": "Alejandro Ochoa ", "_user": "bioc", "_type": "src", "_file": "gcatest_2.13.0.tar.gz", "_fileid": "https://r2.ropensci.org/a213a40265d0b38bdb4f1bb41380e871cba803e226ef16ee4ff003685f02a21c", "_filesize": 2253670, "_sha256": "a213a40265d0b38bdb4f1bb41380e871cba803e226ef16ee4ff003685f02a21c", "_expires": "2027-01-09T11:00:02.000Z", "_created": "2026-10-01T10:55:11.000Z", "_published": "2026-10-01T11:00:05.314Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285", "_status": "success", "_upstream": "https://github.com/bioc/gcatest", "_commit": { "id": "d5181b61f07044840f96242b66a4560f6447136e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381259 }, "_maintainer": { "name": "Alejandro Ochoa", "email": "alejandro.ochoa@duke.edu", "login": "alexviiia", "orcid": "0000-0003-4928-3403", "description": "Statistical geneticist, computational biologist. Well-rounded nerd, also love languages and music.", "uuid": 12603341 }, "_distro": "resolute", "_jobs": [ { "job": 110336025234, "time": 167, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11156356290" }, { "job": 110336025273, "time": 244, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11155813399" }, { "job": 110336025295, "time": 254, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11155428837" }, { "job": 110336025375, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11156495103" }, { "job": 110336025699, "time": 100, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11155179057" }, { "job": 110334775984, "time": 229, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11155209732" }, { "job": 110336025367, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11155943466" }, { "job": 110336025338, "time": 97, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11155688006" }, { "job": 110336025350, "time": 86, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11156435229" }, { "job": 110336025607, "time": 88, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11156217312" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "lfa", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BEDMatrix", "role": "Suggests" }, { "package": "genio", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-05", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.13.0", "bioc": "3.24" }, { "branch": "release", "version": "2.12.0", "bioc": "3.23" } ], "_topics": [ "snp", "dimensionreduction", "principalcomponent", "genomewideassociation" ], "_stars": 7, "_contributors": [ { "user": "alexviiia", "count": 15, "uuid": 12603341 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "jdstorey", "count": 8, "uuid": 6211610 }, { "user": "whao89", "count": 7, "uuid": 5931197 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 471, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 429, "source": "https://www.bioconductor.org/packages/stats/bioc/gcatest" }, "_devurl": "https://github.com/storeylab/gcatest", "_searchresults": 7, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gcatest.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/storeylab/gcatest", "_realowner": "bioc", "_cranurl": false, "_exports": [ "delta_deviance_lf", "gcat", "gcat.stat", "gcatest" ], "_datasets": [ { "name": "sim_geno", "title": "Simulated data from PSD model", "object": "sim_geno", "class": [ "matrix", "array" ], "fields": [], "rows": 10000, "table": true, "tojson": true }, { "name": "sim_trait", "title": "Simulated data from PSD model", "object": "sim_trait", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "delta_deviance_lf", "title": "Calculate delta deviance of logistic null/alternative models", "topics": [ "delta_deviance_lf" ] }, { "page": "gcat", "title": "Genotype Conditional Association TEST", "topics": [ "gcat", "gcat.stat", "gcatest" ] }, { "page": "sim_geno", "title": "Simulated data from PSD model", "topics": [ "sim_geno" ] }, { "page": "sim_trait", "title": "Simulated data from PSD model", "topics": [ "sim_trait" ] } ], "_readme": "https://github.com/bioc/gcatest/raw/HEAD/README.md", "_rundeps": [ "BEDMatrix", "bit", "bit64", "cli", "clipr", "corpcor", "cpp11", "crayon", "crochet", "dplyr", "generics", "genio", "glue", "hms", "lattice", "lfa", "lifecycle", "magrittr", "Matrix", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "Rcpp", "RcppEigen", "readr", "rlang", "RSpectra", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "gcatest.Rmd", "filename": "gcatest.html", "title": "Genotype Conditional Association Test Vignette", "author": "Wei Hao, Minsun Song, Alejandro Ochoa, John D. Storey", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Sample usage", "gcat", "Data Input", "References" ], "created": "2026-01-28 18:23:46", "modified": "2026-01-28 18:23:46", "commits": 1 } ], "_score": 5.498310553789601, "_indexed": true, "_nocasepkg": "gcatest", "_universes": [ "bioc", "alexviiia", "storeylab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.13.0", "date": "2026-10-01T10:59:12.000Z", "distro": "resolute", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/27b9275d79b4d1221f84e912779a81afe86c6a016391f65a134f14c23d368fb1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.6.1", "os": "linux", "version": "2.13.0", "date": "2026-10-01T10:59:26.000Z", "distro": "resolute", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/b9a2151259dc82e59377520c27c325bf2a5ad1d5279a011c2420ce4e1f02e4d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.5.3", "os": "mac", "version": "2.13.0", "date": "2026-10-01T10:57:01.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/2c3edd69ba2e14ab34b18e867ac146b73e3d8583b850eaacdc46155e84440958", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.6.1", "os": "mac", "version": "2.13.0", "date": "2026-10-01T10:56:55.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/440ed9411f15c753f5871fc5948f32ab33f181f9b1f14d87acfc489e679c40c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.6.0", "os": "wasm", "version": "2.13.0", "date": "2026-10-01T10:57:29.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/20e4011526211aabc5290b62712a20f483f4b62c6dcb5f14e590434e42cc84c9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.7.0", "os": "win", "version": "2.13.0", "date": "2026-10-01T10:56:34.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/52998d2a644dcfdaf9a8d26063b695f63596344ceef93814764a7e3e40877997", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.5.3", "os": "win", "version": "2.13.0", "date": "2026-10-01T10:56:24.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/0af085f898bff556d1e8bffc3e9eb2df910a830184f6bf8a33fcc63cb1b45386", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" }, { "r": "4.6.1", "os": "win", "version": "2.13.0", "date": "2026-10-01T10:56:25.000Z", "commit": "d5181b61f07044840f96242b66a4560f6447136e", "fileid": "https://r2.ropensci.org/817f7b9511b86d4220c06684017717cfc0913dcf2c5f2c55b0923d41900a9f9d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36851698285" } ] }