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    "SortBy",
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    "updateAppSessions",
    "uri",
    "userItem",
    "UserOwnedBy",
    "Users"
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      "class": [
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      ],
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      "title": "R SDK for BaseSpace RESTful API",
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        "BaseSpaceR"
      ]
    },
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      "title": "Sample 'AppAuth' instance with 'browse global' scope",
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      ]
    },
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        "appResultCollection-class",
        "appResultItem",
        "appResultItem-class",
        "AppResults",
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        "AppResults-class",
        "AppResultsSummary-class",
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        "countAppResults,Projects-method",
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      ]
    },
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      "title": "'AppSessionAuth' class",
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        "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": [
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        "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": [
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        "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"
      ]
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      "page": "private_methods",
      "title": "Internal methods",
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        "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",
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        "projectItem",
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        "Projects",
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        "$,Response-method",
        "as.list,Collection-method",
        "as.list,Item-method",
        "as.list,Response-method",
        "auth",
        "auth,Response-method",
        "Collection-class",
        "DateCreated",
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        "DateCreated,Item-method",
        "DateCreated,Response-method",
        "DisplayedCount",
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        "DisplayedCount,Item-method",
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        "Href,Item-method",
        "Href,Response-method",
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        "HrefBaseSpaceUI,Item-method",
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        "Id",
        "Id,Collection-method",
        "Id,Item-method",
        "Id,Response-method",
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        "Items",
        "Items,Collection-method",
        "Items,Item-method",
        "Items,Response-method",
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        "length,Item-method",
        "length,Response-method",
        "Limit",
        "Limit,Collection-method",
        "Limit,Item-method",
        "Limit,Response-method",
        "Name",
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        "Response-class",
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        "SortBy",
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        "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",
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        "UserOwnedBy,Response-method",
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        "[,Response-method",
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    },
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        "show,ResponseStatus-method"
      ]
    },
    {
      "page": "Runs-class",
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        "countRuns,AppAuth-method",
        "countRuns,Response-method",
        "listRuns",
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