{
  "_id": "6ad342e8c4bae2fe23391566",
  "Package": "GEOexplorer",
  "Title": "GEOexplorer: a webserver for gene expression analysis and\nvisualisation",
  "Date": "2023/10/31",
  "Version": "1.18.0",
  "Authors@R": "c(person(given = \"Guy\",\nfamily = \"Hunt\",\nrole = c(\"aut\", \"cre\"),\nemail = \"guy.hunt@kcl.ac.uk\",\ncomment = c(ORCID = \"0000-0002-5217-2678\")),\nperson(given = \"Rafael\",\nfamily = \"Henkin\",\nrole = c(\"ctb\", \"ths\"),\nemail = \"r.henkin@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0002-5511-5230\")),\nperson(given = \"Alfredo\",\nfamily = \"Iacoangeli\",\nrole = c(\"ctb\", \"ths\"),\nemail = \"alfredo.iacoangeli@kcl.ac.uk\",\ncomment = c(ORCID = \"0000-0002-5280-5017\")),\nperson(given = \"Fabrizio\",\nfamily = \"Smeraldi\",\nrole = c(\"ctb\", \"ths\"),\nemail = \"f.smeraldi@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0002-0057-8940\")),\nperson(given = \"Michael\",\nfamily = \"Barnes\",\nrole = c(\"ctb\", \"ths\"),\nemail = \"m.r.barnes@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0001-9097-7381\")))",
  "Description": "GEOexplorer is a webserver and R/Bioconductor package and\nweb application that enables users to perform gene expression\nanalysis. The development of GEOexplorer was made possible\nbecause of the excellent code provided by GEO2R (https:\n//www.ncbi.nlm.nih.gov/geo/geo2r/).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/guypwhunt/GEOexplorer/",
  "BugReports": "https://github.com/guypwhunt/GEOexplorer/issues",
  "RoxygenNote": "7.2.3",
  "biocViews": "Software, GeneExpression, mRNAMicroarray,\nDifferentialExpression, Microarray, MicroRNAArray,\nTranscriptomics, RNASeq",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "PackageStatus": "Deprecated",
  "Config/pak/sysreqs": "cmake libfreetype6-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\npython3 libx11-dev zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:56:40 UTC",
  "RemoteUrl": "https://github.com/bioc/GEOexplorer",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 09:30:29 UTC",
    "User": "root"
  },
  "Author": "Guy Hunt [aut, cre] (ORCID: <https://orcid.org/0000-0002-5217-2678>),\nRafael Henkin [ctb, ths] (ORCID:\n<https://orcid.org/0000-0002-5511-5230>),\nAlfredo Iacoangeli [ctb, ths] (ORCID:\n<https://orcid.org/0000-0002-5280-5017>),\nFabrizio Smeraldi [ctb, ths] (ORCID:\n<https://orcid.org/0000-0002-0057-8940>),\nMichael Barnes [ctb, ths] (ORCID:\n<https://orcid.org/0000-0001-9097-7381>)",
  "Maintainer": "Guy Hunt <guy.hunt@kcl.ac.uk>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "GEOexplorer_1.18.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/113c320f3ac1a19a15a7f5e4c6dcd1f45849810b2b66da51466d61f65f96d149",
  "_filesize": 11884358,
  "_sha256": "113c320f3ac1a19a15a7f5e4c6dcd1f45849810b2b66da51466d61f65f96d149",
  "_expires": "2027-01-25T09:41:58.000Z",
  "_created": "2026-10-17T09:30:29.000Z",
  "_published": "2026-10-17T09:42:00.436Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 8
  },
  "_upstream": "https://github.com/bioc/GEOexplorer",
  "_commit": {
    "id": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381000
  },
  "_maintainer": {
    "name": "Guy Hunt",
    "email": "guy.hunt@kcl.ac.uk",
    "login": "guypwhunt",
    "description": "",
    "uuid": 68480973,
    "orcid": "0000-0002-5217-2678"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117363936238,
      "time": 236,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12096479739"
    },
    {
      "job": 117363936096,
      "time": 610,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "12096977797"
    },
    {
      "job": 117363936258,
      "time": 460,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12096951643"
    },
    {
      "job": 117363936157,
      "time": 430,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "12097341305"
    },
    {
      "job": 117363936119,
      "time": 410,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12097336217"
    },
    {
      "job": 117362777538,
      "time": 368,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12096738120"
    },
    {
      "job": 117363936070,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12096522867"
    },
    {
      "job": 117363936099,
      "time": 471,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "12097201862"
    },
    {
      "job": 117363936169,
      "time": 413,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "12097560082"
    },
    {
      "job": 117363936131,
      "time": 576,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12096893156"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "shiny",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "plotly",
      "role": "Depends"
    },
    {
      "package": "enrichR",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "xfun",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "htmltools",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "heatmaply",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "shinyHeatmaply",
      "role": "Imports"
    },
    {
      "package": "shinybusy",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "umap",
      "role": "Imports"
    },
    {
      "package": "GEOquery",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "markdown",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "readxl",
      "role": "Imports"
    },
    {
      "package": "shinycssloaders",
      "role": "Imports"
    },
    {
      "package": "car",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "usethis",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "software",
    "geneexpression",
    "mrnamicroarray",
    "differentialexpression",
    "microarray",
    "micrornaarray",
    "transcriptomics",
    "rnaseq"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "guypwhunt",
      "count": 270,
      "uuid": 68480973
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 272,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GEOexplorer"
  },
  "_devurl": "https://github.com/guypwhunt/geoexplorer",
  "_searchresults": 20,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GEOexplorer.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "loadApp"
  ],
  "_help": [
    {
      "page": "loadApp",
      "title": "A Function to Load the GEOexplorer Shiny App",
      "topics": [
        "loadApp"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GEOexplorer/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "assertthat",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "boot",
    "broom",
    "bslib",
    "ca",
    "cachem",
    "callr",
    "car",
    "carData",
    "cellranger",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "dendextend",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "DT",
    "edgeR",
    "egg",
    "ellipse",
    "emmeans",
    "enrichR",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "flashClust",
    "fontawesome",
    "foreach",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "gclus",
    "genefilter",
    "generics",
    "GenomicRanges",
    "GEOquery",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "heatmaply",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "impute",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "limma",
    "litedown",
    "lme4",
    "lmtest",
    "locfit",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polynom",
    "prettyunits",
    "processx",
    "progress",
    "promises",
    "ps",
    "purrr",
    "qap",
    "quantreg",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppTOML",
    "Rdpack",
    "readr",
    "readxl",
    "reformulas",
    "registry",
    "rematch",
    "rentrez",
    "reshape2",
    "reticulate",
    "rjson",
    "rlang",
    "rmarkdown",
    "rprojroot",
    "RSpectra",
    "RSQLite",
    "rstatix",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "selectr",
    "Seqinfo",
    "seriation",
    "shiny",
    "shinybusy",
    "shinycssloaders",
    "shinyHeatmaply",
    "showtext",
    "showtextdb",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "sysfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "TSP",
    "tzdb",
    "umap",
    "urca",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "webshot",
    "withr",
    "WriteXLS",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "GEOexplorer.Rmd",
      "filename": "GEOexplorer.html",
      "title": "GEOexplorer",
      "author": "Guy Hunt",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Accessing the GEOexplorer Web Server",
        "3. Alternatively Installing the GEOexplorer R package",
        "4. Launching the GEOexplorer R package",
        "3. Tutorial",
        "a. GEOexplorer Structure",
        "I. Home Tab",
        "II. About Tab",
        "III. Workflow Tab",
        "IV. Tutorial Tab",
        "V. GEO Search Tab",
        "VI. Example Datasets Tab",
        "b. Loading GEO Datasets into GEOexplorer",
        "I. Searching for a GEO Dataset",
        "II. Using a GEO Accession Code",
        "c. Performing Exploratory Data Analysis",
        "I. Checking if RNA-seq Datasets Contain Transformed Data",
        "II. Reviewing the Results of Exploratory Data Analysis",
        "d. Performing Differential Gene Expression Analysis",
        "e. Performing Gene Enrichment Analysis",
        "f. Transforming Datasets into the Format Needed by GEOexplorer",
        "I. Identifying that a GEO Dataset Failed to Loaded into GEOexplorer",
        "II. Downloading GEO datasets",
        "g. Uploading a Dataset to GEOexplorer",
        "6. Reporting Problems or Bugs",
        "7. Acknowledgements",
        "8. Session Information"
      ],
      "created": "2021-07-26 08:34:10",
      "modified": "2023-10-11 07:08:41",
      "commits": 6
    }
  ],
  "_score": 4.653212513775344,
  "_indexed": false,
  "_nocasepkg": "geoexplorer",
  "_universes": [
    "bioc-release"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-17T09:36:12.000Z",
      "distro": "resolute",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/23eeef343238b2d5ef4c4cd55942b5bb6914a2e92814eb1ff25917edd6cff331",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-17T09:34:52.000Z",
      "distro": "resolute",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/84105746a4bff7bc41240dbaf6285c919a455d9831a409202e22add4d267972e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.18.0",
      "date": "2026-10-17T09:33:18.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/453aa95a11b255b443288351997ab326e9fa1bc75e0636800a12168722a6eb75",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.18.0",
      "date": "2026-10-17T09:33:19.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/56289e3e6bd1a13aa73b50a7f1c93905dcb95566db68b60a7ed9334e74bc64e5",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.18.0",
      "date": "2026-10-17T09:34:22.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/379ef77b281b11f6a71f27ff7bdf9ebe4df24cb9bf9e567c7e0917de96d3df88",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-17T09:33:46.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/d7baed925c44e3108730d10f4986e0278f02661365f5c793473a3b8852e10cdc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-17T09:33:28.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/708ee4d7359c91271965743d889acdd42ccaf2cb55240f4ce5afecf131bd100e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-17T09:35:52.000Z",
      "commit": "d9177c24e752a90eefcf4807be16ca14e45ba5ea",
      "fileid": "https://r2.ropensci.org/9a4f42d487096edae1df87aa3bda132089a1f896fde1c69e0f220583cc59a47c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39021035301"
    }
  ]
}