| basePath | Class '"HTMLReport"' | 
| basePath-method | Class '"HTMLReport"' | 
| BaseReport-class | Class '"BaseReport"' | 
| baseUrl | Class '"HTMLReport"' | 
| baseUrl-method | Class '"HTMLReport"' | 
| connectionHandlers | Class '"ReportHandlers"' | 
| CSVFile | Function for creating and initializing a CSVFile for publishing results | 
| CSVFile-class | Class '"CSVFile"' | 
| custHeaderPanel | Define a header panel with custom JS/CSS for a Shiny app | 
| DataPackage | Function for creating and initializing an object of class DataPackage. | 
| DataPackage-class | Class '"DataPackage"' | 
| dependencies | Class '"DataPackage"' | 
| dependencies-method | Class '"DataPackage"' | 
| dependencies<- | Class '"DataPackage"' | 
| dependencies<--method | Class '"DataPackage"' | 
| fileHandlers | Class '"ReportHandlers"' | 
| filename | Methods for getting the name of a file for a CSVFile or HTMLReport. | 
| filename-method | Methods for getting the name of a file for a CSVFile or HTMLReport. | 
| filename-methods | Methods for getting the name of a file for a CSVFile or HTMLReport. | 
| fileWIndexHandlers | Class '"ReportHandlers"' | 
| finish | Finalizing reports after publishing results | 
| finish-method | Finalizing reports after publishing results | 
| finish-methods | Finalizing reports after publishing results | 
| HTMLReport | Class '"HTMLReportRef"' | 
| HTMLReport-class | Class '"HTMLReport"' | 
| HTMLReportRef-class | Class '"HTMLReportRef"' | 
| knitrHandlers | Class '"ReportHandlers"' | 
| Link | Create a table of Links | 
| Link-method | Create a table of Links | 
| Link-methods | Create a table of Links | 
| makeOldHTMLReport | Creating and initializing an HTMLReport object | 
| mockRnaSeqData | A counts table of mock RNA-deq data in mouse. | 
| modifyReportDF | Decorate the Basic data.frame Representation of an Object | 
| modifyReportDF-method | Decorate the Basic data.frame Representation of an Object | 
| modifyReportDF-methods | Decorate the Basic data.frame Representation of an Object | 
| name | Class '"BaseReport"' | 
| name-method | Class '"BaseReport"' | 
| name<--method | Class '"BaseReport"' | 
| name<--method | Class '"CSVFile"' | 
| name<--method | Class '"HTMLReport"' | 
| objectToHTML | Transform R objects into HTML form to be inserted in HTML reports | 
| objectToHTML-method | Transform R objects into HTML form to be inserted in HTML reports | 
| objectToHTML-methods | Transform R objects into HTML form to be inserted in HTML reports | 
| page | Class '"HTMLReport"' | 
| page-method | Class '"HTMLReport"' | 
| page<- | Class '"HTMLReport"' | 
| page<--method | Class '"HTMLReport"' | 
| path | Class '"BaseReport"' | 
| path-method | Class '"BaseReport"' | 
| path-method | Class '"DataPackage"' | 
| path-method | Class '"HTMLReport"' | 
| path-method | Class '"HTMLReportRef"' | 
| path-method | Class '"ReportHandlers"' | 
| publish | Methods for publishing a variety of data types in selected output formats | 
| publish-method | Class '"HTMLReportRef"' | 
| publish-method | Methods for publishing a variety of data types in selected output formats | 
| publish-methods | Methods for publishing a variety of data types in selected output formats | 
| readReport | Read in an Existing Report | 
| reportDirectory | Class '"BaseReport"' | 
| reportDirectory-method | Class '"BaseReport"' | 
| reportDirectory<- | Class '"BaseReport"' | 
| reportDirectory<--method | Class '"BaseReport"' | 
| ReportHandlers-class | Class '"ReportHandlers"' | 
| reporting.theme | Color theme for use in ReportingTools | 
| reporting.theme.alternate | Alternate color theme for use in ReportingTools | 
| shinyHandlers | Class '"ReportHandlers"' | 
| show-method | Class '"BaseReport"' | 
| show-method | Class '"HTMLReport"' | 
| show-method | Class '"HTMLReportRef"' | 
| title | Class '"BaseReport"' | 
| title-method | Class '"BaseReport"' | 
| title<- | Class '"BaseReport"' | 
| title<--method | Class '"BaseReport"' | 
| toReportDF | Class Specific Default Behavior for Transforming Objects to data.frames | 
| toReportDF-method | Class Specific Default Behavior for Transforming Objects to data.frames | 
| toReportDF-methods | Class Specific Default Behavior for Transforming Objects to data.frames | 
| url-method | Class '"HTMLReport"' | 
| validConnection | Determine connection validity | 
| [[-method | Class '"HTMLReportRef"' | 
| [[<--method | Class '"HTMLReportRef"' |