{ "_id": "6a1ad0031d7bb097a09e1127", "Package": "GNOSIS", "Type": "Package", "Title": "Genomics explorer using statistical and survival analysis in R", "Version": "1.11.0", "Description": "GNOSIS incorporates a range of R packages enabling users\nto efficiently explore and visualise clinical and genomic data\nobtained from cBioPortal. GNOSIS uses an intuitive GUI and\nmultiple tab panels supporting a range of functionalities.\nThese include data upload and initial exploration, data\nrecoding and subsetting, multiple visualisations, survival\nanalysis, statistical analysis and mutation analysis, in\naddition to facilitating reproducible research.", "Authors@R": "c( \nperson(\"Lydia\", \"King\", ,\"l.king18@universityofgalway.ie\",\nc(\"aut\", \"cre\"), c(ORCID = \"0000-0002-0696-9811\")\n),\nperson(\"Marcel\", \"Ramos\", ,\"marcel.ramos@roswellpark.org\", \"ctb\")\n)", "License": "MIT + file LICENSE", "biocViews": "Software, ShinyApps, Survival, GUI", "BugReports": "https://github.com/Lydia-King/GNOSIS/issues", "URL": "https://github.com/Lydia-King/GNOSIS/", "Video": "https://doi.org/10.5281/zenodo.5788544", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgmp3-dev make\nlibharfbuzz-dev libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libsecret-1-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libmpfr-dev libssl-dev libx11-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:52 UTC", "RemoteUrl": "https://github.com/bioc/GNOSIS", "RemoteRef": "HEAD", "RemoteSha": "2f94c0859ba06369b96b506e148508d82ab60a9b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:15:59 UTC", "User": "root" }, "Author": "Lydia King [aut, cre] (ORCID: ),\nMarcel Ramos [ctb]", "Maintainer": "Lydia King ", "MD5sum": "c2b61fa820a9ffc837195628660b259b", "_user": "bioc", "_type": "src", "_file": "GNOSIS_1.11.0.tar.gz", "_fileid": "db5cb3dedac438c4dcd2b3bcab14e3d4c2dc28f8da20016a0e227b9f54858533", "_filesize": 3397024, "_sha256": "db5cb3dedac438c4dcd2b3bcab14e3d4c2dc28f8da20016a0e227b9f54858533", "_created": "2026-05-30T08:15:59.000Z", "_published": "2026-05-30T11:54:43.925Z", "_jobs": [ { "job": 78636010140, "time": 279, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306788209" }, { "job": 78636010146, "time": 573, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306817051" }, { "job": 78636010169, "time": 523, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306812350" }, { "job": 78636010150, "time": 352, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307984614" }, { "job": 78636010154, "time": 338, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307983217" }, { "job": 78635642608, "time": 427, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306761602" }, { "job": 78636010143, "time": 236, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306783861" }, { "job": 78636010172, "time": 430, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306803393" }, { "job": 78636010148, "time": 468, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306806977" }, { "job": 78636010158, "time": 458, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306806036" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GNOSIS", "_commit": { "id": "2f94c0859ba06369b96b506e148508d82ab60a9b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381312 }, "_maintainer": { "name": "Lydia King", "email": "l.king18@universityofgalway.ie", "orcid": "0000-0002-0696-9811" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "shiny", "role": "Depends" }, { "package": "shinydashboard", "role": "Depends" }, { "package": "shinydashboardPlus", "role": "Depends" }, { "package": "dashboardthemes", "role": "Depends" }, { "package": "shinyWidgets", "role": "Depends" }, { "package": "shinymeta", "role": "Depends" }, { "package": "tidyverse", "role": "Depends" }, { "package": "operator.tools", "role": "Depends" }, { "package": "maftools", "role": "Depends" }, { "package": "DT", "role": "Imports" }, { "package": "fontawesome", "role": "Imports" }, { "package": "shinycssloaders", "role": "Imports" }, { "package": "cBioPortalData", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "survminer", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "compareGroups", "role": "Imports" }, { "package": "rpart", "role": "Imports" }, { "package": "partykit", "role": "Imports" }, { "package": "DescTools", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "rstatix", "role": "Imports" }, { "package": "fabricatr", "role": "Imports" }, { "package": "shinylogs", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.11.0", "bioc": "3.24" }, { "branch": "release", "version": "1.10.0", "bioc": "3.23" } ], "_topics": [ "software", "shinyapps", "survival", "gui" ], "_stars": 7, "_contributors": [ { "user": "lydia-king", "count": 25, "uuid": 64010969 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 268, "source": "https://www.bioconductor.org/packages/stats/bioc/GNOSIS" }, "_devurl": "https://github.com/lydia-king/gnosis", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GNOSIS.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lydia-king/gnosis", "_realowner": "bioc", "_cranurl": false, "_exports": [ "GNOSIS" ], "_help": [ { "page": "GNOSIS", "title": "#' Initialise GNOSIS", "topics": [ "GNOSIS" ] } ], "_readme": "https://github.com/bioc/GNOSIS/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnVIL", "AnVILBase", "anytime", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bookdown", "boot", "broom", "bslib", "BWStest", "cachem", "callr", "car", "carData", "cBioPortalData", "cellranger", "chron", "cigarillo", "class", "cli", "clipr", "codetools", "colorspace", "commonmark", "compareGroups", "conflicted", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "dashboardthemes", "data.table", "DBI", "dbplyr", "DelayedArray", "Deriv", "DescTools", "digest", "DNAcopy", "doBy", "dplyr", "DT", "dtplyr", "e1071", "evaluate", "Exact", "exactRankTests", "expm", "fabricatr", "farver", "fastmap", "filelock", "flextable", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "foreach", "forecast", "formatR", "Formula", "fracdiff", "fresh", "fs", "futile.logger", "futile.options", "future", "future.apply", "gargle", "GCPtools", "gdtools", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicDataCommons", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtext", "gld", "glmnet", "globals", "glue", "gmp", "googledrive", "googlesheets4", "gridExtra", "gridtext", "gtable", "HardyWeinberg", "haven", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "ids", "inum", "IRanges", "isoband", "iterators", "jomo", "jpeg", "jquerylib", "jsonlite", "kableExtra", "KEGGREST", "keyring", "knitr", "kSamples", "labeling", "lambda.r", "later", "lattice", "lazyeval", "libcoin", "lifecycle", "listenv", "litedown", "lme4", "lmom", "lmtest", "lubridate", "maftools", "magrittr", "markdown", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "maxstat", "memoise", "mgcv", "mice", "microbenchmark", "mime", "miniUI", "minqa", "mitml", "modelr", "multcompView", "MultiAssayExperiment", "mvtnorm", "nanotime", "nlme", "nloptr", "nnet", "numDeriv", "officer", "openssl", "operator.tools", "ordinal", "otel", "pan", "parallelly", "partykit", "pbkrtest", "pheatmap", "pillar", "pkgconfig", "plyr", "PMCMRplus", "png", "polynom", "prettyunits", "processx", "progress", "promises", "proxy", "ps", "purrr", "quantreg", "R.cache", "R.methodsS3", "R.oo", "R.utils", "R6", "ragg", "RaggedExperiment", "rapiclient", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppCCTZ", "RcppDate", "RcppEigen", "RCurl", "Rdpack", "readr", "readxl", "reformulas", "rematch", "rematch2", "reprex", "reshape2", "restfulr", "Rhtslib", "rjson", "RJSONIO", "rlang", "rmarkdown", "rmdformats", "Rmpfr", "rootSolve", "rpart", "rprojroot", "Rsamtools", "Rsolnp", "RSQLite", "rstatix", "rstudioapi", "RTCGAToolbox", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "selectr", "Seqinfo", "shape", "shiny", "shinycssloaders", "shinydashboard", "shinydashboardPlus", "shinyjs", "shinylogs", "shinymeta", "shinyWidgets", "snow", "sourcetools", "SparseArray", "SparseM", "stringi", "stringr", "styler", "SummarizedExperiment", "SuppDists", "survival", "survminer", "svglite", "sys", "systemfonts", "TCGAutils", "textshaping", "tibble", "tidyr", "tidyselect", "tidyverse", "timechange", "timeDate", "tinytex", "truncnorm", "tzdb", "ucminf", "UCSC.utils", "urca", "utf8", "uuid", "vctrs", "viridisLite", "vroom", "waiter", "withr", "writexl", "xfun", "XML", "xml2", "xtable", "XVector", "yaml", "zip", "zoo" ], "_vignettes": [ { "source": "GNOSIS.Rmd", "filename": "GNOSIS.html", "title": "GNOSIS: Genomics explorer using statistical and survival analysis in R", "author": "Lydia King", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading the package", "Launching GNOSIS", "GNOSIS layout", "Data upload and preview", "Data reformatting and filtering", "Data visualisation", "Statistical and survival analysis", "Mutation Analysis", "Input Log", "Additional Resources", "Session Info" ], "created": "2023-09-04 08:37:13", "modified": "2023-10-14 16:31:35", "commits": 5 } ], "_score": 4.845098040014257, "_indexed": true, "_nocasepkg": "gnosis", "_universes": [ "bioc", "lydia-king" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T08:21:18.000Z", "distro": "noble", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "3cc7b05801e7ec8c8a6bcd24602ab67c8ff954501254c31d2b673219abf5cc49", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.6.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T08:20:57.000Z", "distro": "noble", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "9bb7ffe54b4d82ddaf2bd59d1c6815302d7663e01ef0312dad9e2c17bc77d8f0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-05-30T11:50:17.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "f0685f4d53f37dab8ee708b47e5df56f03554d9739c0b416e14a21b051c5c5e4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.6.0", "os": "mac", "version": "1.11.0", "date": "2026-05-30T11:50:08.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "d868b1605064c6d8af7076d59e556cf230095416782648c877034990e834e0fb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.6.0", "os": "wasm", "version": "1.11.0", "date": "2026-05-30T08:20:50.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "a3fe510c16f6342db9484e24b3e889a3883822794c461daf9f4f3351c2bcd2c2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.7.0", "os": "win", "version": "1.11.0", "date": "2026-05-30T08:18:46.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "48701f1de2486bd73d54d0c53515bf2a99e7d024fb070aa4a70f2f0120da55fd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.5.3", "os": "win", "version": "1.11.0", "date": "2026-05-30T08:19:32.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "24c7828ae183bcbd1a4c7ec9c222cd8d2c7d46506fe4850305494f7ae6bf9582", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" }, { "r": "4.6.0", "os": "win", "version": "1.11.0", "date": "2026-05-30T08:18:55.000Z", "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b", "fileid": "90b041e820b592f4397dabc21bb6edd457e0265b06c4eeb4937ce2eebc9e160b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678880751" } ] }