{
  "_id": "6a1e9b221d7bb097a0a6e5eb",
  "Package": "bioCancer",
  "Title": "Interactive Multi-Omics Cancers Data Visualization and Analysis",
  "Version": "1.41.0",
  "Date": "2024-02-14",
  "Authors@R": "person(\"Karim\", \"Mezhoud\", role=c(\"aut\", \"cre\"), email=\"kmezhoud@gmail.com\")",
  "Description": "This package is a Shiny App to visualize and analyse\ninteractively Multi-Assays of Cancer Genomic Data.",
  "VignetteBuilder": "knitr",
  "URL": "https://kmezhoud.github.io/bioCancer/",
  "BugReports": "https://github.com/kmezhoud/bioCancer/issues",
  "License": "AGPL-3 | file LICENSE",
  "LazyData": "true",
  "biocViews": "GUI, DataRepresentation, Network, MultipleComparison,\nPathways, Reactome, Visualization,GeneExpression,GeneTarget",
  "RoxygenNote": "7.3.1",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libsecret-1-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:36 UTC",
  "RemoteUrl": "https://github.com/bioc/bioCancer",
  "RemoteRef": "HEAD",
  "RemoteSha": "adaad4e79a716bc4546389870a19a50d2e590c12",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:45:27 UTC",
    "User": "root"
  },
  "Author": "Karim Mezhoud [aut, cre]",
  "Maintainer": "Karim Mezhoud <kmezhoud@gmail.com>",
  "MD5sum": "fa6d892f18a2e2680f58691db00195c4",
  "_user": "bioc",
  "_type": "src",
  "_file": "bioCancer_1.41.0.tar.gz",
  "_fileid": "f59c1495d73f16c8dbe707830d5a25b46626d89c04b4877026a1987890c0628f",
  "_filesize": 10083789,
  "_sha256": "f59c1495d73f16c8dbe707830d5a25b46626d89c04b4877026a1987890c0628f",
  "_created": "2026-06-02T08:45:27.000Z",
  "_published": "2026-06-02T08:58:10.913Z",
  "_jobs": [
    {
      "job": 79033340714,
      "time": 331,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7353188420"
    },
    {
      "job": 79033340660,
      "time": 628,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7353289804"
    },
    {
      "job": 79033340674,
      "time": 675,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7353306647"
    },
    {
      "job": 79033340830,
      "time": 517,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7353251954"
    },
    {
      "job": 79033340711,
      "time": 402,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7353213132"
    },
    {
      "job": 79031982167,
      "time": 479,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7353068482"
    },
    {
      "job": 79033340684,
      "time": 343,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7353192387"
    },
    {
      "job": 79033340943,
      "time": 555,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7353265831"
    },
    {
      "job": 79033340666,
      "time": 481,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7353239566"
    },
    {
      "job": 79033340699,
      "time": 494,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7353244269"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 6,
    "note": 17
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/bioCancer",
  "_commit": {
    "id": "adaad4e79a716bc4546389870a19a50d2e590c12",
    "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": 1777380216
  },
  "_maintainer": {
    "name": "Karim Mezhoud",
    "email": "kmezhoud@gmail.com",
    "login": "kmezhoud",
    "description": "Data Scientist",
    "uuid": 4458195
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "radiant.data",
      "version": ">= 0.9.1",
      "role": "Depends"
    },
    {
      "package": "cBioPortalData",
      "role": "Depends"
    },
    {
      "package": "XML",
      "version": ">= 3.98",
      "role": "Depends"
    },
    {
      "package": "R.oo",
      "role": "Imports"
    },
    {
      "package": "R.methodsS3",
      "role": "Imports"
    },
    {
      "package": "DT",
      "version": ">= 0.3",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 0.7.2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "version": ">= 1.0.5",
      "role": "Imports"
    },
    {
      "package": "AlgDesign",
      "version": ">= 1.1.7.3",
      "role": "Imports"
    },
    {
      "package": "import",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "shinythemes",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "geNetClassifier",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "org.Bt.eg.db",
      "role": "Imports"
    },
    {
      "package": "DOSE",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Imports"
    },
    {
      "package": "reactome.db",
      "role": "Imports"
    },
    {
      "package": "ReactomePA",
      "role": "Imports"
    },
    {
      "package": "DiagrammeR",
      "version": "<= 1.01",
      "role": "Imports"
    },
    {
      "package": "visNetwork",
      "role": "Imports"
    },
    {
      "package": "htmlwidgets",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 0.10.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "gui",
    "datarepresentation",
    "network",
    "multiplecomparison",
    "pathways",
    "reactome",
    "visualization",
    "geneexpression",
    "genetarget",
    "analysis",
    "biocancer-interface",
    "cancer",
    "cancer-studies",
    "rmarkdown"
  ],
  "_stars": 21,
  "_contributors": [
    {
      "user": "vnijs",
      "count": 1244,
      "uuid": 2998956
    },
    {
      "user": "kmezhoud",
      "count": 313,
      "uuid": 4458195
    },
    {
      "user": "mostly-harmless",
      "count": 6,
      "uuid": 25526758
    },
    {
      "user": "rsm-aaa111",
      "count": 1,
      "uuid": 138641414
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 390,
    "source": "https://www.bioconductor.org/packages/stats/bioc/bioCancer"
  },
  "_devurl": "https://github.com/kmezhoud/biocancer",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/bioCancer.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kmezhoud/biocancer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "attriColorGene",
    "attriColorValue",
    "attriColorVector",
    "attriShape2Gene",
    "attriShape2Node",
    "bioCancer",
    "CGDS",
    "checkDimensions",
    "coffeewheel",
    "coffeewheelOutput",
    "displayTable",
    "Edges_Diseases_obj",
    "findPhantom",
    "getEvidenceCodes",
    "getFreqMutData",
    "getGenesClassification",
    "getList_Cases",
    "getList_GenProfs",
    "getListProfData",
    "getOrthologs",
    "getProfData",
    "getSequensed_SampleSize",
    "mapLists",
    "metabologram",
    "metabologramOutput",
    "Mutation_obj",
    "Node_df_FreqIn",
    "Node_Diseases_obj",
    "Node_obj_CNA_ProfData",
    "Node_obj_FreqIn",
    "Node_obj_Met_ProfData",
    "Node_obj_mRNA_Classifier",
    "pickGO",
    "pickRefSeq",
    "removeNAs",
    "renderCoffeewheel",
    "renderMetabologram",
    "reStrColorGene",
    "reStrDimension",
    "reStrDisease",
    "Studies_obj",
    "test.CGDS",
    "translate",
    "UnifyRowNames",
    "whichGeneList",
    "widgetThumbnail"
  ],
  "_datasets": [
    {
      "name": "epiGenomics",
      "title": "Default dataset of bioCancer",
      "object": "epiGenomics",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Diseases",
        "Genes",
        "mRNA",
        "RPPA",
        "Met450",
        "CNA",
        "FreqMut"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    },
    {
      "name": "user_CNA",
      "title": "Example of Copy Number Alteration (CNA) dataset",
      "object": "user_CNA",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "ATM",
        "ATR",
        "BRCA1",
        "BRCA2",
        "CHEK1",
        "CHEK2",
        "FANCF",
        "MDC1",
        "MLH1",
        "MSH2",
        "PARP1",
        "RAD51"
      ],
      "rows": 579,
      "table": true,
      "tojson": true
    },
    {
      "name": "user_MetHM27",
      "title": "Example of Methylation HM27 dataset",
      "object": "user_MetHM27",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "ATM",
        "ATR",
        "BRCA1",
        "BRCA2",
        "CHEK1",
        "CHEK2",
        "FANCF",
        "MDC1",
        "MLH1",
        "MSH2",
        "PARP1",
        "RAD51"
      ],
      "rows": 600,
      "table": true,
      "tojson": true
    },
    {
      "name": "user_MetHM450",
      "title": "Example of Methylation HM450 dataset",
      "object": "user_MetHM450",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "ATM",
        "ATR",
        "BRCA1",
        "BRCA2",
        "CHEK1",
        "CHEK2",
        "FANCF",
        "MDC1",
        "MLH1",
        "MSH2",
        "PARP1",
        "RAD51"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "user_mRNA",
      "title": "Example of mRNA expression dataset",
      "object": "user_mRNA",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "ATM",
        "ATR",
        "BRCA1",
        "BRCA2",
        "CHEK1",
        "CHEK2",
        "FANCF",
        "MDC1",
        "MLH1",
        "MSH2",
        "PARP1",
        "RAD51"
      ],
      "rows": 307,
      "table": true,
      "tojson": true
    },
    {
      "name": "user_Mut",
      "title": "Example of Mutation dataset",
      "object": "user_Mut",
      "class": [
        "data.frame"
      ],
      "fields": [
        ".id",
        "entrez_gene_id",
        "gene_symbol",
        "case_id",
        "sequencing_center",
        "mutation_status",
        "mutation_type",
        "validation_status",
        "amino_acid_change",
        "functional_impact_score",
        "xvar_link",
        "xvar_link_pdb",
        "xvar_link_msa",
        "chr",
        "start_position",
        "end_position",
        "reference_allele",
        "variant_allele",
        "reference_read_count_tumor",
        "variant_read_count_tumor",
        "reference_read_count_normal",
        "variant_read_count_normal",
        "genetic_profile_id"
      ],
      "rows": 37,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-dbEscapeString",
      "title": "Private Escape string",
      "topics": [
        ".dbEscapeString"
      ]
    },
    {
      "page": "dot-getTableName",
      "title": "Gets the table name from the INPARANOID style genus names.",
      "topics": [
        ".getTableName"
      ]
    },
    {
      "page": "dot-pickRef",
      "title": "Secret function that does the magic for pickRefSeq.",
      "topics": [
        ".pickRef"
      ]
    },
    {
      "page": "AnnotationFuncs",
      "title": "Annotation translation functions",
      "topics": [
        "AnnotationFuncs"
      ]
    },
    {
      "page": "attriColorGene",
      "title": "Attribute Color to Gene",
      "topics": [
        "attriColorGene"
      ]
    },
    {
      "page": "attriColorValue",
      "title": "Attribute Color to Value",
      "topics": [
        "attriColorValue"
      ]
    },
    {
      "page": "attriColorVector",
      "title": "Attribute color to a vector of numeric values",
      "topics": [
        "attriColorVector"
      ]
    },
    {
      "page": "attriShape2Gene",
      "title": "Attribute shape to nodes",
      "topics": [
        "attriShape2Gene"
      ]
    },
    {
      "page": "attriShape2Node",
      "title": "Attributes shape to Nodes",
      "topics": [
        "attriShape2Node"
      ]
    },
    {
      "page": "bioCancer",
      "title": "Launch bioCancer with default browser",
      "topics": [
        "-package",
        "bioCancer"
      ]
    },
    {
      "page": "CGDS",
      "title": "CGDS connect object to cBioPortal",
      "topics": [
        "CGDS"
      ]
    },
    {
      "page": "checkDimensions",
      "title": "Check wich Cases and genetic profiles are available for selected study",
      "topics": [
        "checkDimensions"
      ]
    },
    {
      "page": "coffeewheel",
      "title": "This is an htmlwidgets-based visualization tool for hierarchical data. It is zoomable, meaning that you can interact with the hierarchy and zoom in/out accordingly.",
      "topics": [
        "coffeewheel"
      ]
    },
    {
      "page": "coffeewheelOutput",
      "title": "Widget output function for use in Shiny",
      "topics": [
        "coffeewheelOutput"
      ]
    },
    {
      "page": "displayTable",
      "title": "Display dataframe in table using DT package",
      "topics": [
        "displayTable"
      ]
    },
    {
      "page": "Edges_Diseases_obj",
      "title": "get Edges dataframe for Gene/Disease association from geNetClassifier",
      "topics": [
        "Edges_Diseases_obj"
      ]
    },
    {
      "page": "epiGenomics",
      "title": "Default dataset of bioCancer",
      "topics": [
        "epiGenomics"
      ]
    },
    {
      "page": "findPhantom",
      "title": "Check if PhantomJS is installed. Similar to webshot",
      "topics": [
        "findPhantom"
      ]
    },
    {
      "page": "getEvidenceCodes",
      "title": "Returns GO evidence codes.",
      "topics": [
        "getEvidenceCodes"
      ]
    },
    {
      "page": "getFreqMutData",
      "title": "get mutation frequency",
      "topics": [
        "getFreqMutData"
      ]
    },
    {
      "page": "getGenesClassification",
      "title": "get genes classification",
      "topics": [
        "getGenesClassification"
      ]
    },
    {
      "page": "getList_Cases",
      "title": "get list of cases of each selected study in Classifier panel",
      "topics": [
        "getList_Cases"
      ]
    },
    {
      "page": "getList_GenProfs",
      "title": "get list of genetic profiles of each selected study in Classifier panel",
      "topics": [
        "getList_GenProfs"
      ]
    },
    {
      "page": "getListProfData",
      "title": "get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)",
      "topics": [
        "getListProfData"
      ]
    },
    {
      "page": "getOrthologs",
      "title": "Performs quicker lookup for orthologs in homologe data packages",
      "topics": [
        "getOrthologs"
      ]
    },
    {
      "page": "getProfData",
      "title": "search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)",
      "topics": [
        "getProfData"
      ]
    },
    {
      "page": "getSequensed_SampleSize",
      "title": "get samples size of sequensed genes",
      "topics": [
        "getSequensed_SampleSize"
      ]
    },
    {
      "page": "mapLists",
      "title": "Replaces contents of list A with elements of list B",
      "topics": [
        "mapLists"
      ]
    },
    {
      "page": "metabologram",
      "title": "Circular plot of hierarchital data of genetic profile.",
      "topics": [
        "metabologram"
      ]
    },
    {
      "page": "metabologramOutput",
      "title": "Widget output function for use in Shiny",
      "topics": [
        "metabologramOutput"
      ]
    },
    {
      "page": "Mutation_obj",
      "title": "Atribute mutation frequency to nodes",
      "topics": [
        "Mutation_obj"
      ]
    },
    {
      "page": "Node_df_FreqIn",
      "title": "Attributes size to Nodes depending on number of interaction",
      "topics": [
        "Node_df_FreqIn"
      ]
    },
    {
      "page": "Node_Diseases_obj",
      "title": "Attributes color and shape to Nodes of Diseases",
      "topics": [
        "Node_Diseases_obj"
      ]
    },
    {
      "page": "Node_obj_CNA_ProfData",
      "title": "Attribute CNA data to node border",
      "topics": [
        "Node_obj_CNA_ProfData"
      ]
    },
    {
      "page": "Node_obj_FreqIn",
      "title": "Attribute interaction frequency to node size",
      "topics": [
        "Node_obj_FreqIn"
      ]
    },
    {
      "page": "Node_obj_Met_ProfData",
      "title": "Attribute gene Methylation to Nodes",
      "topics": [
        "Node_obj_Met_ProfData"
      ]
    },
    {
      "page": "Node_obj_mRNA_Classifier",
      "title": "Atrribute genes expression to color nodes",
      "topics": [
        "Node_obj_mRNA_Classifier"
      ]
    },
    {
      "page": "pickGO",
      "title": "Cleans up result from org.Xx.egGO and returns specific GO identifiers",
      "topics": [
        "pickGO"
      ]
    },
    {
      "page": "pickRefSeq",
      "title": "Picks a prioritised RefSeq identifier from a list of identifiers",
      "topics": [
        "pickRefSeq"
      ]
    },
    {
      "page": "removeNAs",
      "title": "Removes entries equal 'NA' from list or vector",
      "topics": [
        "removeNAs"
      ]
    },
    {
      "page": "renderCoffeewheel",
      "title": "Widget render function for use in Shiny",
      "topics": [
        "renderCoffeewheel"
      ]
    },
    {
      "page": "renderMetabologram",
      "title": "Widget render function for use in Shiny",
      "topics": [
        "renderMetabologram"
      ]
    },
    {
      "page": "reStrColorGene",
      "title": "Restructure the list of color attributed to the genes in every dimenssion for every studies",
      "topics": [
        "reStrColorGene"
      ]
    },
    {
      "page": "reStrDimension",
      "title": "Restructure the list of color attributed to the genes in every study for every dimensions",
      "topics": [
        "reStrDimension"
      ]
    },
    {
      "page": "reStrDisease",
      "title": "Restructure the list of color attributed to the genes in every disease",
      "topics": [
        "reStrDisease"
      ]
    },
    {
      "page": "returnTextAreaInput",
      "title": "Return message when the filter formula is not correct (mRNA > 500)",
      "topics": [
        "returnTextAreaInput"
      ]
    },
    {
      "page": "Studies_obj",
      "title": "get object for grViz. Link Studies to genes",
      "topics": [
        "Studies_obj"
      ]
    },
    {
      "page": "switchButton",
      "title": "A function to change the Original checkbox of rshiny into a nice true/false or on/off switch button No javascript involved. Only CSS code.",
      "topics": [
        "switchButton"
      ]
    },
    {
      "page": "test.CGDS",
      "title": "S3 method to test cBioPortal connection",
      "topics": [
        "test.CGDS"
      ]
    },
    {
      "page": "translate",
      "title": "Translate between different identifiers",
      "topics": [
        "translate"
      ]
    },
    {
      "page": "UnifyRowNames",
      "title": "Unify row names in data frame with the same order of gene list.",
      "topics": [
        "UnifyRowNames"
      ]
    },
    {
      "page": "user_CNA",
      "title": "Example of Copy Number Alteration (CNA) dataset",
      "topics": [
        "user_CNA"
      ]
    },
    {
      "page": "user_MetHM27",
      "title": "Example of Methylation HM27 dataset",
      "topics": [
        "user_MetHM27"
      ]
    },
    {
      "page": "user_MetHM450",
      "title": "Example of Methylation HM450 dataset",
      "topics": [
        "user_MetHM450"
      ]
    },
    {
      "page": "user_mRNA",
      "title": "Example of mRNA expression dataset",
      "topics": [
        "user_mRNA"
      ]
    },
    {
      "page": "user_Mut",
      "title": "Example of Mutation dataset",
      "topics": [
        "user_Mut"
      ]
    },
    {
      "page": "whichGeneList",
      "title": "Verify which gene list is selected",
      "topics": [
        "whichGeneList"
      ]
    },
    {
      "page": "widgetThumbnail",
      "title": "Capture html output widget as .png in R",
      "topics": [
        "widgetThumbnail"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/bioCancer/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "aisdk",
    "AlgDesign",
    "AnnotationDbi",
    "AnVIL",
    "AnVILBase",
    "ape",
    "aplot",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "callr",
    "car",
    "carData",
    "cBioPortalData",
    "cellranger",
    "cigarillo",
    "class",
    "cli",
    "clipr",
    "cluster",
    "clusterProfiler",
    "codetools",
    "colorspace",
    "commonmark",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "Deriv",
    "DiagrammeR",
    "digest",
    "dir.expiry",
    "doBy",
    "DOSE",
    "dplyr",
    "DT",
    "e1071",
    "EBarrays",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "GCPtools",
    "gdtools",
    "generics",
    "geNetClassifier",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicDataCommons",
    "GenomicFeatures",
    "GenomicRanges",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggraph",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "GPArotation",
    "graph",
    "graphite",
    "graphlayouts",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "import",
    "infotheo",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "keyring",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "litedown",
    "lme4",
    "lmtest",
    "lubridate",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minet",
    "miniUI",
    "minqa",
    "mnormt",
    "modelr",
    "MultiAssayExperiment",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "org.Bt.eg.db",
    "org.Hs.eg.db",
    "otel",
    "patchwork",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "prettyunits",
    "processx",
    "progress",
    "promises",
    "proxy",
    "ps",
    "psych",
    "purrr",
    "quantreg",
    "qvalue",
    "R.methodsS3",
    "R.oo",
    "R6",
    "radiant.data",
    "RaggedExperiment",
    "randomizr",
    "rapiclient",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RCurl",
    "Rdpack",
    "reactome.db",
    "ReactomePA",
    "readr",
    "readxl",
    "reformulas",
    "rematch",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "RJSONIO",
    "rlang",
    "rmarkdown",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "RTCGAToolbox",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "selectr",
    "Seqinfo",
    "shiny",
    "shinyAce",
    "shinyFiles",
    "shinythemes",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "TCGAutils",
    "tibble",
    "tidydr",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timechange",
    "timeDate",
    "tinytex",
    "treeio",
    "tweenr",
    "tzdb",
    "UCSC.utils",
    "urca",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "visNetwork",
    "vroom",
    "withr",
    "writexl",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "bioCancer.Rmd",
      "filename": "bioCancer.html",
      "title": "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and Analysis",
      "author": "\\ Karim Mezhoud \\ \\ Nuclear Science Center of Tunisia, Nuclear Safety & Security Department",
      "engine": "knitr::rmarkdown",
      "headings": [
        "bioCancer Package",
        "Pipeline Overview",
        "How to run bioCancer",
        "Portal Panel",
        "Display available Cancer Studies in Table",
        "Studies Panel",
        "Browse the data",
        "Sort",
        "Filters in Table",
        "Global Search",
        "Column filter",
        "Download table as csv file",
        "Side bar Menu",
        "Studies List",
        "Cases and Genetic Profiles for selected study",
        "Gene List Examples",
        "Show Clinical Data in Table",
        "Side bar menu",
        "Select variables to show",
        "Load Clinical Data to Datasets (to Processing Panel)",
        "Show Profiles Data in Table",
        "Load Gene List",
        "Load Profiles to Datasets",
        "Processing Panel",
        "Manage data and state: Load data into bioCancer, Save data to disk, Remove a dataset from memory, or Save/Load the full state of the app",
        "Datasets",
        "Load data",
        "Save data",
        "Save and load state",
        "Remove data from memory",
        "Using commands to load and save data",
        "Show data in table form",
        "Select columns",
        "Filter",
        "Column filters and Search",
        "Visualize data",
        "Plot-type",
        "Box plots",
        "Sub-plots and heat-maps",
        "Line, loess, and jitter",
        "Axis scale",
        "Flip axes",
        "Plot height and width",
        "Customizing plots in R > Report",
        "Create pivot tables to explore your data",
        "Summarize and explore your data",
        "Transform command log",
        "Type",
        "Transform",
        "Create",
        "Recode",
        "Rename",
        "Replace",
        "Clipboard",
        "Normalize",
        "Reorder or remove columns",
        "Reorder or remove levels",
        "Remove missing values",
        "Remove duplicates",
        "Show duplicates",
        "Combine two datasets",
        "Inner join (superheroes, publishers)",
        "Left join (superheroes, publishers)",
        "Right join (superheroes, publishers)",
        "Full join (superheroes, publishers)",
        "Semi join (superheroes, publishers)",
        "Anti join (superheroes, publishers)",
        "Dataset order",
        "Inner join (publishers, superheroes)",
        "Left and Right join (publishers, superheroes)",
        "Full join (publishers, superheroes)",
        "Semi join (publishers, superheroes)",
        "Anti join (publishers, superheroes)",
        "Additional tools to combine datasets (avengers, superheroes)",
        "Bind rows",
        "Bind columns",
        "Intersect",
        "Union",
        "Setdiff",
        "Enrichment Panel",
        "Show multi-Omics Data in Circular Layout",
        "Studies in Wheel",
        "Load Profiles in Datasets",
        "Genes / Diseases / Pathways Classification and clustering",
        "Classification",
        "Plot Clusters",
        "Gene Diseases Association",
        "Function Interaction Network Enrichment",
        "Edges Attributes",
        "Function Interactions (FIs) Type",
        "Use Linkers",
        "Layouts",
        "dot",
        "twopi",
        "neato",
        "circo",
        "Nodes Attributes",
        "From ReactomeFI",
        "From Classifier",
        "mRNA",
        "Studies",
        "From Profiles Data",
        "Legend",
        "Interpretation",
        "References"
      ],
      "created": "2016-05-20 08:54:13",
      "modified": "2023-09-29 16:53:02",
      "commits": 6
    }
  ],
  "_score": 5.799340549453582,
  "_indexed": true,
  "_nocasepkg": "biocancer",
  "_universes": [
    "bioc",
    "kmezhoud"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-06-02T08:52:03.000Z",
      "distro": "noble",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "bece0d43642b2e3598fde01ba58e47dcb31d486933127930ba26ce09440cc68b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-06-02T08:52:20.000Z",
      "distro": "noble",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "fd76268aeb6f6c0b6a8fc133a47ae7f6cd90c8471910cf0f468314057b09e279",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-06-02T08:49:47.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "546b0875c907e1fd11cc6de966ac0e6df94685a901ae6203a95b6ecbc4a9e6a4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-06-02T08:49:18.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "200f46873ff5a154393ffd1bfaa3486a13c54f67bee48d40cb6c61feeb2375ca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-06-02T08:52:06.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "111c71ea7dcd8f9371a014545ef8455a490356e2c96b1a39d3d7606c00df482e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-06-02T08:50:19.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "b944e8f98819aa2cfad7e68f765046064310c93d0898833d95769edfed8a22bf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-06-02T08:49:25.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "66eec0feabeffe7daa5414bf07395cfd311c877e6f26f781fa47b48a39d636f7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-06-02T08:49:25.000Z",
      "commit": "adaad4e79a716bc4546389870a19a50d2e590c12",
      "fileid": "25afa2424e228852ee2ffd4f8b7f2db1170db352e4e20d3cb7d45f9556f019c4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808464570"
    }
  ]
}