{ "_id": "6a194b2bacfb0bcc41ddca19", "Package": "gwasurvivr", "Type": "Package", "Title": "gwasurvivr: an R package for genome wide survival analysis", "Version": "1.30.0", "Author": "Abbas Rizvi, Ezgi Karaesmen, Martin Morgan, Lara\nSucheston-Campbell", "Maintainer": "Abbas Rizvi ", "Description": "gwasurvivr is a package to perform survival analysis using\nCox proportional hazard models on imputed genetic data.", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "URL": "https://github.com/suchestoncampbelllab/gwasurvivr", "biocViews": "GenomeWideAssociation, Survival, Regression, Genetics, SNP,\nGeneticVariability, Pharmacogenomics, BiomedicalInformatics", "RoxygenNote": "6.1.0", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev libx11-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:48:10 UTC", "RemoteUrl": "https://github.com/bioc/gwasurvivr", "RemoteRef": "RELEASE_3_23", "RemoteSha": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:08:26 UTC", "User": "root" }, "MD5sum": "fa21dd6271c9000e95176b3a7acb260d", "_user": "bioc-release", "_type": "src", "_file": "gwasurvivr_1.30.0.tar.gz", "_fileid": "a6ae6f79d00e11040b3dbfad3f18ad55f712985c520a30b55af7f417f1443486", "_filesize": 177224, "_sha256": "a6ae6f79d00e11040b3dbfad3f18ad55f712985c520a30b55af7f417f1443486", "_created": "2026-05-29T07:08:26.000Z", "_published": "2026-05-29T08:15:39.807Z", "_jobs": [ { "job": 78454674175, "time": 300, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285154507" }, { "job": 78454674236, "time": 525, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285216020" }, { "job": 78454674232, "time": 460, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285197812" }, { "job": 78454674177, "time": 297, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7286188784" }, { "job": 78454674132, "time": 305, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7286185668" }, { "job": 78453867873, "time": 377, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285078560" }, { "job": 78454674144, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285122824" }, { "job": 78454674181, "time": 441, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285192638" }, { "job": 78454674157, "time": 381, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285176494" }, { "job": 78454674225, "time": 434, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285190578" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/gwasurvivr", "_commit": { "id": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "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": 1777380490 }, "_maintainer": { "name": "Abbas Rizvi", "email": "aarizv@gmail.com", "login": "aarizvi", "description": "Data Scientist @ Tempus", "uuid": 11141478 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "GWASTools", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "SNPRelate", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "genomewideassociation", "survival", "regression", "genetics", "snp", "geneticvariability", "pharmacogenomics", "biomedicalinformatics" ], "_stars": 13, "_contributors": [ { "user": "aarizvi", "count": 314, "uuid": 11141478 }, { "user": "karaesmen", "count": 75, "uuid": 19581853 }, { "user": "markplatts", "count": 28, "uuid": 22068402 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 384, "source": "https://www.bioconductor.org/packages/stats/bioc/gwasurvivr" }, "_mentions": 1, "_devurl": "https://github.com/suchestoncampbelllab/gwasurvivr", "_searchresults": 77, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gwasurvivr.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/suchestoncampbelllab/gwasurvivr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "gdsCoxSurv", "impute2CoxSurv", "michiganCoxSurv", "plinkCoxSurv", "sangerCoxSurv" ], "_help": [ { "page": "gdsCoxSurv", "title": "Fit Cox survival to all variants from a standard IMPUTE2 output after genotype imputation", "topics": [ "gdsCoxSurv" ] }, { "page": "impute2CoxSurv", "title": "Fit Cox survival to all variants from a standard IMPUTE2 output after genotype imputation", "topics": [ "impute2CoxSurv" ] }, { "page": "michiganCoxSurv", "title": "Fit Cox survival to all variants in a .vcf.gz file from Michigan imputation server", "topics": [ "michiganCoxSurv" ] }, { "page": "plinkCoxSurv", "title": "Fit Cox survival to all variants from PLINK binary files (.BED, .BIM, .FAM)", "topics": [ "plinkCoxSurv" ] }, { "page": "sangerCoxSurv", "title": "Fit Cox survival to all variants in a .vcf.gz file from Sanger imputation server", "topics": [ "sangerCoxSurv" ] } ], "_readme": "https://github.com/bioc/gwasurvivr/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "backports", "BH", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "broom", "BSgenome", "cachem", "cigarillo", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "DNAcopy", "dplyr", "fastmap", "forcats", "foreach", "formatR", "formula.tools", "futile.logger", "futile.options", "gdsfmt", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glmnet", "glue", "GWASExactHW", "GWASTools", "haven", "hms", "httr", "IRanges", "iterators", "jomo", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "lme4", "lmtest", "logistf", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "mice", "mime", "minqa", "mitml", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "operator.tools", "ordinal", "pan", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "quantreg", "quantsmooth", "R6", "rbibutils", "Rcpp", "RcppEigen", "RCurl", "Rdpack", "readr", "reformulas", "restfulr", "RhpcBLASctl", "Rhtslib", "rjson", "rlang", "rpart", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "sandwich", "Seqinfo", "shape", "snow", "SNPRelate", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "ucminf", "utf8", "VariantAnnotation", "vctrs", "vroom", "withr", "XML", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "gwasurvivr_Introduction.Rmd", "filename": "gwasurvivr_Introduction.html", "title": "gwasurvivr Vignette", "author": "Abbas Rizvi, Ezgi Karaesmen, Martin Morgan, Lara Sucheston-Campbell", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Main input arguments", "Main output format", "Getting started", "Dependencies", "User settings: parallelization setup", "R Session Examples", "Michigan Imputation Server", "Single SNP analysis", "SNP with covariate interaction", "Sanger Imputation Server", "IMPUTE2 Imputation", "SNP covariate interaction", "plinkCoxSurv", "Batch Examples", "Batch Example sangerCoxSurv", "Batch Example impute2CoxSurv", "Batch Example michiganCoxSurv", "Session info", "References" ], "created": "2018-05-17 19:17:19", "modified": "2018-10-04 18:20:23", "commits": 9 } ], "_score": 6.477555332198982, "_indexed": false, "_nocasepkg": "gwasurvivr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/gwasurvivr", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.30.0", "date": "2026-05-29T07:13:05.000Z", "distro": "noble", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "fbd1fa30873fa0da7fb06dabc4ef41c1c02f70f4c8d87efc5c42b987acdae8f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.6.0", "os": "linux", "version": "1.30.0", "date": "2026-05-29T07:12:21.000Z", "distro": "noble", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "87bba3f4740fe13fe0fdb8ecbc195fa54577f805006aa8b87dde953b61ea5ccb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.5.3", "os": "mac", "version": "1.30.0", "date": "2026-05-29T08:11:49.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "9edb6686cc398a36338c3cd6fac019307e01e55ffe3f1304871abd1d737f842b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.6.0", "os": "mac", "version": "1.30.0", "date": "2026-05-29T08:11:44.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "f0cd3f703fee326facc4258fac1ef479ab5538db914f60997726804259ae058c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.6.0", "os": "wasm", "version": "1.30.0", "date": "2026-05-29T07:12:08.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "5e43b8252668453f11692a005989ede6b1f45122dfa61d5f392ef473389d9f30", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.7.0", "os": "win", "version": "1.30.0", "date": "2026-05-29T07:11:15.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "cf2833201cfc7b23ff2159c19a59039c9e6a55a0b4c74c11c631abebbc9fb88a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.5.3", "os": "win", "version": "1.30.0", "date": "2026-05-29T07:10:57.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "3b98a8fd27c558f7ce66f8e46916ac72c0766c787d120fdc5a0fac85cabb583f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" }, { "r": "4.6.0", "os": "win", "version": "1.30.0", "date": "2026-05-29T07:11:19.000Z", "commit": "63578a19491875ca6b8a9ccbcce2bb7b0846b8de", "fileid": "883d2f1654ee045c6dafcbb942c956c17063def0469d93f7c31e6483d190f287", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623250390" } ] }