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 1.14.0

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.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.