{
  "_id": "6a57190bff0138dec5d6db72",
  "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": "2026-07-15 05:11:31 UTC",
    "User": "root"
  },
  "Author": "Lydia King [aut, cre] (ORCID: <https://orcid.org/0000-0002-0696-9811>),\nMarcel Ramos [ctb]",
  "Maintainer": "Lydia King <l.king18@universityofgalway.ie>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GNOSIS_1.11.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7cbe059071367078a2ea91ab2c94720de87286899cff6578504b8e4325267fc4",
  "_filesize": 3398425,
  "_sha256": "7cbe059071367078a2ea91ab2c94720de87286899cff6578504b8e4325267fc4",
  "_expires": "2026-10-23T05:22:16.000Z",
  "_created": "2026-07-15T05:11:31.000Z",
  "_published": "2026-07-15T05:22:18.785Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 7
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128",
  "_status": "success",
  "_upstream": "https://github.com/bioc/GNOSIS",
  "_commit": {
    "id": "2f94c0859ba06369b96b506e148508d82ab60a9b",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "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": "resolute",
  "_jobs": [
    {
      "job": 87273881260,
      "time": 290,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8333257415"
    },
    {
      "job": 87273881256,
      "time": 531,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8333322061"
    },
    {
      "job": 87273881275,
      "time": 564,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8333330875"
    },
    {
      "job": 87273881252,
      "time": 245,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8333245353"
    },
    {
      "job": 87273881255,
      "time": 360,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8333276107"
    },
    {
      "job": 87272890486,
      "time": 408,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8333177818"
    },
    {
      "job": 87273881242,
      "time": 254,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8333247360"
    },
    {
      "job": 87273881282,
      "time": 418,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8333291304"
    },
    {
      "job": 87273881264,
      "time": 444,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8333299130"
    },
    {
      "job": 87273881279,
      "time": 412,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8333289502"
    }
  ],
  "_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",
    "followers": 446,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 272,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GNOSIS"
  },
  "_devurl": "https://github.com/lydia-king/gnosis",
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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",
    "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": "2026-07-15T05:17:01.000Z",
      "distro": "resolute",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/b858a457028c34df4aed9008a268e073666dcc89eafd2e5e0948be030f1f9cb3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-07-15T05:16:55.000Z",
      "distro": "resolute",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/4133b02c5953623ac847c965acbc0495cda32c2c77efe0c47c7f238a4379c92d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-07-15T05:13:48.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/874e09458b4d120f42924793cc5716aeb2ad975020d9d9ac95c381f1ae1f779c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-07-15T05:14:12.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/33dbe5865634fc4860085833f7ed473d1799157e979bd5a5a1af7907fbb370e9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-07-15T05:16:36.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/58f6077a9faa54bffdd6d5b026bb57f4f495a456071c8fcc584dc0a497ca8d9b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-15T05:14:12.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/9f49e3d16dafe9b96d7ca336ef3aa94250f340f1c4288a5373ebcbff6576b980",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-15T05:14:13.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/a0567b0eefd92456e9285facd4eb3c5c0c6f06383a30397904436dcade1c0157",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-07-15T05:14:10.000Z",
      "commit": "2f94c0859ba06369b96b506e148508d82ab60a9b",
      "fileid": "https://r2.ropensci.org/a53a808e3323d5a5118440f4c819d61a9d8760e94dc16d31e386460f28904ed3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29390557128"
    }
  ]
}