Browse and Query Clinical and Genomic Data from cBioPortal
Get all available clinical attribute IDs for a study
Get Available Gene Panels For a Database
Get All Patient IDs in a Study
Get Available Genomic Profiles For a Study or Database
Get All Sample Lists Available For a Study
Get All Sample IDs in a Study
Get Metadata on All Available Studies in a Database
cbioportalR: Browse and Query Clinical and Genomic Data from cBioPorta...
Core function to retrieve data from cBioPortal API.
Get clinical data by attribute, study ID and sample ID
Get clinical data by attribute, study ID and patient ID
Internal Function to Get Mutations/CNA/Fusion By Sample ID
Internal Function to Get Mutations/CNA/Fusion By Study ID
Get Gene Name Alias for a Given Hugo Symbol
Get cBioPortal Access Token
Get clinical data by attribute, study ID and patient ID
Get clinical data by attribute, study ID and sample ID
Get all available clinical data for a specified study
Get CNA By Sample ID
Get CNA By Study
Get Entrez Gene ID for a given set of Hugo Symbols
Get Fusions By Sample ID
Get Fusions By Study
Retrieve Genes Included For a Specified Panel ID
Get A List of Genes for a Specified Database
Get All Genomic Information By Sample IDs
Get All Genomic Information By Study
Get Hugo Symbol for a given set of Entrez IDs
Get Mutations By Sample ID
Get Mutations By Study ID
Get Gene Panel by study ID and sample ID
Get sample IDs for a given set of patient IDs
Get Copy Number Segmentation Data By Sample ID
Get Copy Number Segmentation Data By Study
Get Metadata on All Available Studies in Database or a Specified Study
Default value for NULL.
Pipe operator
Connect to cBioPortal DB
Test the Database Connection Anytime During your R Session
Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints <https://www.cbioportal.org/api/swagger-ui/index.html>. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See <https://www.cbioportal.org/> and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.
Useful links