| .validation_dependencies | Validation Dependencies |
| addColumn_Server | Server logic of module for adding a column |
| addColumn_UI | UI elements of module for adding a column |
| addRowRc_Server | Server logic of Resource tab module for adding a row |
| addRowRc_UI | UI elements of Resource tab module for adding a row |
| addRow_Server | Server logic of module for adding a row |
| addRow_UI | UI elements of module for adding a row |
| cBioPortalToDataFrame | Convert the cBioPortal sample- and patient-data file format into a data.frame |
| cbpManager | Launch cbpManager |
| cbpManager-pkg | cbpManager |
| check_input_dates | Check the input of dates |
| convertDataFrame | Convert the data.frame to the appropriate file format for cBioPortal |
| create_name | Sanitize names |
| deleteColumn_Server | Server logic of module for deleting a column |
| deleteColumn_UI | UI elements of module for deleting a column |
| deleteRowRc_Server | Server logic of Resource tab module for deleting a row |
| deleteRowRc_UI | UI elements of module for removing a row |
| deleteRow_Server | Server logic of module for removing a row |
| deleteRow_UI | UI elements of module for removing a row |
| editRowRc_Server | Server logic of Resource tab module for editing a row |
| editRowRc_UI | UI elements of module for editing a row |
| editRow_Server | Server logic of module for editing a row |
| editRow_UI | UI elements of module for editing a row |
| fncols | Add empty column to a data.frame, if column does not exist in the data.frame |
| generateOncotreeUIwidgets | Create shiny UI-widget for specific columns of oncotree entries |
| generateUIwidgets | Generate UI input widget |
| getSampleIDs | Get Sample IDs associated with Patient IDs from the data_clinical_sample.txt file |
| importPatientData | Import patient data into current study data.frames |
| IsDate | Check if input is in the appropriate date format |
| saveResource_Server | Server logic of module for saving the resource data |
| saveResource_UI | UI elements of module for saving the resource data |
| saveTimeline_Server | Server logic of module for saving the source data |
| saveTimeline_UI | UI elements of module for saving the data |
| setupConda_cbpManager | Install conda environment with basilisk before launching the app |
| shinyAppServer | Shiny app server function |
| shinyAppUI | Shiny app server object create the shiny application user interface |
| updateOncotreeUIwidgets | Updates UI-widgets for specific columns of oncotree entries |
| validateResourceDefinition | Validate resource_definition input |
| validateResourcePatient | Validate resource_patient input |
| validateResourceSample | Validate resource_sample input |
| validateResourceStudy | Validate resource_study input |
| ValidationDependencies | Validation Dependencies |
| writeLogfile | Write a line to a logfile containing the date, time, username (from Shinyproxy), and the name of the modified file. |