{
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  "Package": "BaseSpaceR",
  "Title": "R SDK for BaseSpace RESTful API",
  "Description": "A rich R interface to Illumina's BaseSpace cloud computing\nenvironment, enabling the fast development of data analysis and\nvisualisation tools.",
  "Version": "1.56.0",
  "Author": "Adrian Alexa",
  "Maintainer": "Jared O'Connell <joconnell@illumina.com>",
  "biocViews": "Infrastructure, DataRepresentation, ConnectTools, Software,\nDataImport, HighThroughputSequencing, Sequencing, Genetics",
  "License": "Apache License 2.0",
  "Collate": "generics.R misc.R ServiceURI.R Error.R AppAuth.R\nAppSessionAuth.R Href.R Properties.R Response.R Users.R Runs.R\nGenomes.R Projects.R AppResults.R AppSessions.R Samples.R\nFiles.R Files_extra.R Variants.R Coverage.R zzz.R",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:30 UTC",
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    "dataimport",
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    "sequencing",
    "genetics"
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    "name": "Bioconductor",
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    "appResultCollection",
    "appResultItem",
    "AppResults",
    "AppSessions",
    "as.list",
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    "authNativeClient",
    "authWebClient",
    "countAppResults",
    "countAppSessions",
    "countFiles",
    "countGenomes",
    "countProjects",
    "countRuns",
    "countSamples",
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    "createProject",
    "DateCreated",
    "DisplayedCount",
    "fileCollection",
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    "genomeCollection",
    "genomeItem",
    "Genomes",
    "getBAMs",
    "getCoverage",
    "getCoverageStats",
    "getFiles",
    "getIndexedBam",
    "getVariants",
    "getVariantSet",
    "hasAccess",
    "Href",
    "HrefBaseSpaceUI",
    "Id",
    "initializeAuth",
    "Items",
    "Limit",
    "listAppResults",
    "listAppSessions",
    "listFiles",
    "listGenomes",
    "listProjects",
    "listRuns",
    "listSamples",
    "Name",
    "Offset",
    "performOAuth",
    "projectCollection",
    "projectItem",
    "Projects",
    "putFiles",
    "requestAccessToken",
    "ResponseStatus",
    "runCollection",
    "runItem",
    "Runs",
    "sampleCollection",
    "sampleItem",
    "Samples",
    "ServiceURI",
    "show",
    "SortBy",
    "SortDir",
    "Status",
    "TotalCount",
    "updateAppSessions",
    "uri",
    "userItem",
    "UserOwnedBy",
    "Users"
  ],
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    {
      "name": "aAuth",
      "title": "Sample 'AppAuth' instance with 'browse global' scope",
      "object": "aAuth",
      "file": "aAuth.rda",
      "class": [
        "AppAuth"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
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    {
      "page": "BaseSpaceR-package",
      "title": "R SDK for BaseSpace RESTful API",
      "topics": [
        "BaseSpaceR-package",
        "BaseSpaceR"
      ]
    },
    {
      "page": "data-aAuth",
      "title": "Sample 'AppAuth' instance with 'browse global' scope",
      "topics": [
        "aAuth"
      ]
    },
    {
      "page": "AppAuth-class",
      "title": "'AppAuth' class",
      "topics": [
        "AppAuth",
        "AppAuth-class",
        "hasAccess",
        "hasAccess,AppAuth-method",
        "initializeAuth",
        "initializeAuth,AppAuth-method",
        "performOAuth",
        "requestAccessToken",
        "requestAccessToken,AppAuth-method"
      ]
    },
    {
      "page": "AppResults-class",
      "title": "'AppResults' and '\"AppResultsSummary\"' objects",
      "topics": [
        "appResultCollection",
        "appResultCollection-class",
        "appResultItem",
        "appResultItem-class",
        "AppResults",
        "AppResults,AppAuth-method",
        "AppResults,AppResultsSummary-method",
        "AppResults,missing-method",
        "AppResults-class",
        "AppResultsSummary-class",
        "countAppResults",
        "countAppResults,AppAuth-method",
        "countAppResults,Projects-method",
        "countAppResults,ProjectsSummary-method",
        "countAppResults,Response-method",
        "createAppResults",
        "createAppResults,AppAuth-method",
        "createAppResults,Projects-method",
        "listAppResults",
        "listAppResults,AppAuth-method",
        "listAppResults,Projects-method"
      ]
    },
    {
      "page": "AppSessionAuth",
      "title": "'AppSessionAuth' class",
      "topics": [
        "AppSessionAuth-class",
        "authNativeClient",
        "authWebClient"
      ]
    },
    {
      "page": "AppSessions-class",
      "title": "'AppSessions' object",
      "topics": [
        "appSessionItem",
        "appSessionItem-class",
        "AppSessions",
        "AppSessions,AppAuth-method",
        "AppSessions,AppResults-method",
        "AppSessions-class",
        "countAppSessions",
        "countAppSessions,AppAuth-method",
        "countAppSessions,Response-method",
        "listAppSessions",
        "listAppSessions,AppAuth-method",
        "updateAppSessions",
        "updateAppSessions,AppAuth-method"
      ]
    },
    {
      "page": "Coverage",
      "title": "Methods for accessing coverage data from BAM files",
      "topics": [
        "getCoverage",
        "getCoverage,AppAuth-method",
        "getCoverageStats",
        "getCoverageStats,AppAuth-method"
      ]
    },
    {
      "page": "Files-class",
      "title": "'Files' and 'FilesSummary' objects",
      "topics": [
        "countFiles",
        "countFiles,AppAuth-method",
        "countFiles,AppResults-method",
        "countFiles,AppResultsSummary-method",
        "countFiles,Response-method",
        "countFiles,Runs-method",
        "countFiles,RunsSummary-method",
        "countFiles,Samples-method",
        "countFiles,SamplesSummary-method",
        "fileCollection",
        "fileCollection-class",
        "fileItem",
        "fileItem-class",
        "Files",
        "Files,AppAuth-method",
        "Files,FilesSummary-method",
        "Files,missing-method",
        "Files-class",
        "FilesSummary-class",
        "getFiles",
        "getFiles,AppAuth-method",
        "listFiles",
        "listFiles,AppAuth-method",
        "listFiles,AppResults-method",
        "listFiles,AppResultsSummary-method",
        "listFiles,Runs-method",
        "listFiles,RunsSummary-method",
        "listFiles,Samples-method",
        "listFiles,SamplesSummary-method",
        "putFiles",
        "putFiles,AppAuth-method"
      ]
    },
    {
      "page": "FilesExtra",
      "title": "High-level methods for 'Files' objects and related",
      "topics": [
        "getBAMs",
        "getBAMs,AppResults-method",
        "getIndexedBam"
      ]
    },
    {
      "page": "Genomes-class",
      "title": "'Genomes' and 'GenomesSummary' objects",
      "topics": [
        "countGenomes",
        "genomeCollection",
        "genomeCollection-class",
        "genomeItem",
        "genomeItem-class",
        "Genomes",
        "Genomes,AppAuth-method",
        "Genomes,GenomesSummary-method",
        "Genomes,missing-method",
        "Genomes-class",
        "GenomesSummary-class",
        "listGenomes",
        "listGenomes,AppAuth-method",
        "listGenomes,Response-method"
      ]
    },
    {
      "page": "private_methods",
      "title": "Internal methods",
      "topics": [
        "as.character,staticHref-method",
        "auth,Href-method",
        "show,Href-method",
        "show,staticHref-method"
      ]
    },
    {
      "page": "Projects-class",
      "title": "'Projects' and 'ProjectsSummary' objects",
      "topics": [
        "countProjects",
        "countProjects,AppAuth-method",
        "countProjects,Response-method",
        "createProject",
        "createProject,AppAuth-method",
        "listProjects",
        "listProjects,AppAuth-method",
        "listProjects,Response-method",
        "projectCollection",
        "projectCollection-class",
        "projectItem",
        "projectItem-class",
        "Projects",
        "Projects,AppAuth-method",
        "Projects,missing-method",
        "Projects,ProjectsSummary-method",
        "Projects-class",
        "ProjectsSummary-class"
      ]
    },
    {
      "page": "Response-class",
      "title": "'Item', 'Collection' and 'Response' objects",
      "topics": [
        "$,Collection-method",
        "$,Item-method",
        "$,Response-method",
        "as.list,Collection-method",
        "as.list,Item-method",
        "as.list,Response-method",
        "auth",
        "auth,Response-method",
        "Collection-class",
        "DateCreated",
        "DateCreated,Collection-method",
        "DateCreated,Item-method",
        "DateCreated,Response-method",
        "DisplayedCount",
        "DisplayedCount,Collection-method",
        "DisplayedCount,Item-method",
        "DisplayedCount,Response-method",
        "Href",
        "Href,Collection-method",
        "Href,Item-method",
        "Href,Response-method",
        "HrefBaseSpaceUI",
        "HrefBaseSpaceUI,Collection-method",
        "HrefBaseSpaceUI,Item-method",
        "HrefBaseSpaceUI,Response-method",
        "Id",
        "Id,Collection-method",
        "Id,Item-method",
        "Id,Response-method",
        "Item-class",
        "Items",
        "Items,Collection-method",
        "Items,Item-method",
        "Items,Response-method",
        "length,Collection-method",
        "length,Item-method",
        "length,Response-method",
        "Limit",
        "Limit,Collection-method",
        "Limit,Item-method",
        "Limit,Response-method",
        "Name",
        "Name,Collection-method",
        "Name,Item-method",
        "Name,Response-method",
        "Offset",
        "Offset,Collection-method",
        "Offset,Item-method",
        "Offset,Response-method",
        "Response-class",
        "show,Collection-method",
        "show,Item-method",
        "show,Response-method",
        "SortBy",
        "SortBy,Collection-method",
        "SortBy,Item-method",
        "SortBy,Response-method",
        "SortDir",
        "SortDir,Collection-method",
        "SortDir,Item-method",
        "SortDir,Response-method",
        "Status",
        "Status,Collection-method",
        "Status,Item-method",
        "Status,Response-method",
        "TotalCount",
        "TotalCount,Collection-method",
        "TotalCount,Item-method",
        "TotalCount,Response-method",
        "UserOwnedBy",
        "UserOwnedBy,Collection-method",
        "UserOwnedBy,Item-method",
        "UserOwnedBy,Response-method",
        "[,Collection-method",
        "[,Response-method",
        "[[,Collection,numeric-method",
        "[[,Response,ANY-method"
      ]
    },
    {
      "page": "Error",
      "title": "Class '\"ResponseStatus\"'",
      "topics": [
        "ResponseStatus",
        "ResponseStatus-class",
        "show,ResponseStatus-method"
      ]
    },
    {
      "page": "Runs-class",
      "title": "'Runs' and 'RunsSummary' objects",
      "topics": [
        "countRuns",
        "countRuns,AppAuth-method",
        "countRuns,Response-method",
        "listRuns",
        "listRuns,AppAuth-method",
        "listRuns,Response-method",
        "runCollection",
        "runCollection-class",
        "runItem",
        "runItem-class",
        "Runs",
        "Runs,AppAuth-method",
        "Runs,missing-method",
        "Runs,RunsSummary-method",
        "Runs-class",
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    },
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      "page": "Samples-class",
      "title": "'Samples' and 'SamplesSummary' objects",
      "topics": [
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        "countSamples,AppAuth-method",
        "countSamples,Projects-method",
        "countSamples,ProjectsSummary-method",
        "countSamples,Response-method",
        "listSamples",
        "listSamples,AppAuth-method",
        "listSamples,Projects-method",
        "sampleCollection",
        "sampleCollection-class",
        "sampleItem",
        "sampleItem-class",
        "Samples",
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        "Samples,SamplesSummary-method",
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        "SamplesSummary-class"
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      "page": "ServiceURI-class",
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        "ServiceURI-class",
        "show,ServiceURI-method",
        "uri",
        "uri,ServiceURI-method"
      ]
    },
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      "page": "Users-class",
      "title": "'Users' objects and resources",
      "topics": [
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        "userItem-class",
        "Users",
        "Users,AppAuth-method",
        "Users,missing-method",
        "Users,Response-method",
        "Users-class"
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    {
      "page": "Variants",
      "title": "Methods for accessing varinant data",
      "topics": [
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        "getVariantSet",
        "getVariantSet,AppAuth-method"
      ]
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