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

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Documentation for package ‘cbpManager’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.