# Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics

## Documentation for package ‘cbpManager’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.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.