{ "_id": "6a1ff020b401979e73441ead", "Package": "GRAB", "Type": "Package", "Title": "Genome-Wide Robust Analysis for Biobank Data (GRAB)", "Version": "0.2.4", "Date": "2025-12-04", "Authors@R": "c(person(given = \"Wenjian\",\nfamily = \"Bi\",\nrole = \"aut\"),\nperson(given = \"Wei\",\nfamily = \"Zhou\",\nrole = \"aut\"),\nperson(given = \"Rounak\",\nfamily = \"Dey\",\nrole = \"aut\"),\nperson(given = \"Zhangchen\",\nfamily = \"Zhao\",\nrole = \"aut\"),\nperson(given = \"Seunggeun\",\nfamily = \"Lee\",\nrole = \"aut\"),\nperson(given = \"Woody\",\nfamily = \"Miao\",\nrole = \"cre\",\nemail = \"miaolin@pku.edu.cn\"))", "Description": "Provides a comprehensive suite of genome-wide association\nstudy (GWAS) methods specifically designed for biobank-scale\ndata, including but not limited to, robust approaches for\ntime-to-event traits (Li et al., 2025\n) and ordinal categorical\ntraits (Bi et al., 2021 ). The\npackage also offers general frameworks for GWAS of any trait\ntype (Bi et al., 2020 ), while\naccounting for sample relatedness (Xu et al., 2025\n) or population structure (Ma\net al., 2025 ). By accurately\napproximating score statistic distributions using saddlepoint\napproximation (SPA), these methods can effectively control type\nI error rates for rare variants and in the presence of\nunbalanced phenotype distributions. Additionally, the package\nincludes functions for simulating genotype and phenotype data\nto support research and method development.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-03 09:06:52 UTC", "User": "root" }, "Author": "Wenjian Bi [aut], Wei Zhou [aut], Rounak Dey [aut], Zhangchen\nZhao [aut], Seunggeun Lee [aut], Woody Miao [cre]", "Maintainer": "Woody Miao ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-12-05 11:40:32 UTC", "RemoteUrl": "https://github.com/cran/GRAB", "RemoteRef": "HEAD", "RemoteSha": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "MD5sum": "ce9754ec499947700243c4e723b44827", "_user": "cran", "_type": "src", "_file": "GRAB_0.2.4.tar.gz", "_fileid": "2e5106a5731252d804a7c91d0156b1654f2208fef84b2f21bb565105748d9e60", "_filesize": 1959204, "_sha256": "2e5106a5731252d804a7c91d0156b1654f2208fef84b2f21bb565105748d9e60", "_created": "2026-06-03T09:06:52.000Z", "_published": "2026-06-03T09:13:04.095Z", "_distro": "noble", "_jobs": [ { "job": 79259755430, "time": 236, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7380384697" }, { "job": 79259755251, "time": 223, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7380378586" }, { "job": 79259755209, "time": 243, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7380386170" }, { "job": 79259755180, "time": 235, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7380382587" }, { "job": 79258914749, "time": 287, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7380297162" }, { "job": 79259755261, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7380353136" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/GRAB", "_commit": { "id": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "author": "Woody Miao ", "committer": "cran-robot ", "message": "version 0.2.4\n", "time": 1764934832 }, "_maintainer": { "name": "Woody Miao", "email": "miaolin@pku.edu.cn", "login": "woodymiao", "description": "", "uuid": 18162272 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "ordinal", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "RcppParallel", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "SKAT", "role": "Suggests" }, { "package": "dbplyr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "R.utils", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-34", "n": 1 }, { "week": "2025-49", "n": 1 } ], "_tags": [ { "name": "0.2.1", "date": "2025-07-25" }, { "name": "0.2.2", "date": "2025-07-29" }, { "name": "0.2.3", "date": "2025-08-20" }, { "name": "0.2.4", "date": "2025-12-05" } ], "_stars": 0, "_contributors": [ { "user": "woodymiao", "count": 4, "uuid": 18162272 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 144, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GRAB" }, "_searchresults": 113, "_topics": [ "zlib", "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GRAB.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/woodymiao/grab", "_realowner": "woodymiao", "_cranurl": false, "_releases": [ { "version": "0.2.1", "date": "2025-07-25" }, { "version": "0.2.2", "date": "2025-08-01" }, { "version": "0.2.3", "date": "2025-08-20" }, { "version": "0.2.4", "date": "2025-12-11" } ], "_exports": [ "CCT", "getPairwiseIBD", "getSparseGRM", "getTempFilesFullGRM", "GRAB.getGenoInfo", "GRAB.makePlink", "GRAB.Marker", "GRAB.NullModel", "GRAB.POLMM", "GRAB.POLMM.Region", "GRAB.ReadGeno", "GRAB.Region", "GRAB.SAGELD", "GRAB.SimubVec", "GRAB.SimuGMat", "GRAB.SimuGMatFromGenoFile", "GRAB.SimuPheno", "GRAB.SPACox", "GRAB.SPAGRM", "GRAB.SPAmix", "GRAB.WtCoxG", "SAGELD.NullModel", "SPAGRM.NullModel" ], "_help": [ { "page": "CCT", "title": "Cauchy Combination Test for p-value aggregation", "topics": [ "CCT" ] }, { "page": "getPairwiseIBD", "title": "Calculate Pairwise IBD (Identity By Descent)", "topics": [ "getPairwiseIBD" ] }, { "page": "getSparseGRM", "title": "Make a 'SparseGRMFile' for 'GRAB.NullModel'.", "topics": [ "getSparseGRM" ] }, { "page": "getTempFilesFullGRM", "title": "Make temporary files to be passed to function 'getSparseGRM'.", "topics": [ "getTempFilesFullGRM" ] }, { "page": "GRAB.getGenoInfo", "title": "Get allele frequency and missing rate information from genotype data", "topics": [ "GRAB.getGenoInfo" ] }, { "page": "GRAB.makePlink", "title": "Convert genotype matrix to PLINK format files", "topics": [ "GRAB.makePlink" ] }, { "page": "GRAB.Marker", "title": "Perform single-marker association tests using a fitted null model", "topics": [ "GRAB.Marker" ] }, { "page": "GRAB.NullModel", "title": "Top-level API for generating a null model object used by GRAB.Marker and GRAB.Region", "topics": [ "GRAB.NullModel" ] }, { "page": "GRAB.POLMM", "title": "Instruction of POLMM method", "topics": [ "GRAB.POLMM" ] }, { "page": "GRAB.POLMM.Region", "title": "Instruction of POLMM-GENE method", "topics": [ "GRAB.POLMM.Region" ] }, { "page": "GRAB.ReadGeno", "title": "Read genotype data from multiple file formats", "topics": [ "GRAB.ReadGeno" ] }, { "page": "GRAB.Region", "title": "Perform region-based association tests", "topics": [ "GRAB.Region" ] }, { "page": "GRAB.SAGELD", "title": "SAGELD method in GRAB package", "topics": [ "GRAB.SAGELD" ] }, { "page": "GRAB.SimubVec", "title": "Simulate random effects based on family structure", "topics": [ "GRAB.SimubVec" ] }, { "page": "GRAB.SimuGMat", "title": "Simulate genotype data matrix for related and unrelated subjects", "topics": [ "GRAB.SimuGMat" ] }, { "page": "GRAB.SimuGMatFromGenoFile", "title": "Simulate genotype matrix from external genotype file", "topics": [ "GRAB.SimuGMatFromGenoFile" ] }, { "page": "GRAB.SimuPheno", "title": "Simulate phenotypes from linear predictors", "topics": [ "GRAB.SimuPheno" ] }, { "page": "GRAB.SPACox", "title": "Instruction of SPACox method", "topics": [ "GRAB.SPACox" ] }, { "page": "GRAB.SPAGRM", "title": "Instruction of SPAGRM method", "topics": [ "GRAB.SPAGRM" ] }, { "page": "GRAB.SPAmix", "title": "Instruction of SPAmix method", "topics": [ "GRAB.SPAmix" ] }, { "page": "GRAB.WtCoxG", "title": "Instruction of WtCoxG method", "topics": [ "GRAB.WtCoxG" ] }, { "page": "SAGELD.NullModel", "title": "Construct SAGELD/GALLOP null model from a mixed-effects fit", "topics": [ "SAGELD.NullModel" ] }, { "page": "SPAGRM.NullModel", "title": "Fit SPAGRM null model from residuals and relatedness inputs", "topics": [ "SPAGRM.NullModel" ] } ], "_readme": "https://github.com/cran/GRAB/raw/HEAD/README.md", "_rundeps": [ "BH", "bit", "bit64", "blob", "boot", "cachem", "cli", "cpp11", "data.table", "DBI", "dplyr", "fastmap", "generics", "glue", "igraph", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "memoise", "minqa", "mvtnorm", "nlme", "nloptr", "numDeriv", "ordinal", "pillar", "pkgconfig", "R6", "rbibutils", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rdpack", "reformulas", "rlang", "RSQLite", "survival", "tibble", "tidyselect", "ucminf", "utf8", "vctrs", "withr" ], "_sysdeps": [ { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg-3.1ubuntu2.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "liblapack", "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": "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" } ], "_score": 3.354108439147401, "_indexed": false, "_nocasepkg": "grab", "_universes": [ "cran" ], "_indexurl": "https://woodymiao.r-universe.dev/GRAB", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.4", "date": "2026-06-03T09:10:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "fileid": "f67f965468bd3c4bd15b6146cd063f59339db6852ebe5643fa83c3bb748de4b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681" }, { "r": "4.7.0", "os": "linux", "version": "0.2.4", "date": "2026-06-03T09:10:31.000Z", "distro": "noble", "arch": "x86_64", "commit": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "fileid": "9563a54cffbb1c38ff3c1a52ba23834ed74a7cc4be58aac30c1ca28fa8654a7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681" }, { "r": "4.6.0", "os": "linux", "version": "0.2.4", "date": "2026-06-03T09:10:42.000Z", "distro": "noble", "arch": "aarch64", "commit": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "fileid": "2d61481e9f4b874403e2ff1eeda38b5e0d1ca0317b3ce12f6bcb0493552bd04b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681" }, { "r": "4.6.0", "os": "linux", "version": "0.2.4", "date": "2026-06-03T09:10:35.000Z", "distro": "noble", "arch": "x86_64", "commit": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "fileid": "3e831a6698382b844ce6d5a610e98b961a44ce9a1dd19ccdb505928b0d38474b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.4", "date": "2026-06-03T09:10:36.000Z", "arch": "emscripten", "commit": "2f9cfb43ff584ada36abcb8f686b0e5398cbc230", "fileid": "c81cbb935ec960d6e029e0bf1dc853025fde4f07a5b3e7abc7642924aff762c5", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26874726681" } ] }