# Browse and Query Clinical and Genomic Data from cBioPortal

## Documentation for package ‘cbioportalR’ version 1.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

available_clinical_attributes | Get all available clinical attribute IDs for a study
available_gene_panels | Get Available Gene Panels For a Database
available_patients | Get All Patient IDs in a Study
available_profiles | Get Available Genomic Profiles For a Study or Database
available_samples | Get All Sample IDs in a Study
available_sample_lists | Get All Sample Lists Available For a Study
available_studies | Get Metadata on All Available Studies in a Database
get_alias | Get Gene Name Alias for a Given Hugo Symbol
get_cbioportal_token | Get cBioPortal Access Token
get_clinical_by_patient | Get clinical data by attribute, study ID and patient ID
get_clinical_by_sample | Get clinical data by attribute, study ID and sample ID
get_clinical_by_study | Get all available clinical data for a specified study
get_cna_by_sample | Get CNA By Sample ID
get_cna_by_study | Get CNA By Study
get_entrez_id | Get Entrez Gene ID for a given set of Hugo Symbols
get_fusions_by_sample | Get Fusions By Sample ID
get_fusions_by_study | Get Fusions By Study
get_genes | Get A List of Genes for a Specified Database
get_genetics_by_sample | Get All Genomic Information By Sample IDs
get_genetics_by_study | Get All Genomic Information By Study
get_gene_panel | Retrieve Genes Included For a Specified Panel ID
get_hugo_symbol | Get Hugo Symbol for a given set of Entrez IDs
get_mutations_by_sample | Get Mutations By Sample ID
get_mutations_by_study | Get Mutations By Study ID
get_panel_by_sample | Get Gene Panel by study ID and sample ID
get_samples_by_patient | Get sample IDs for a given set of patient IDs
get_segments_by_sample | Get Copy Number Segmentation Data By Sample ID
get_segments_by_study | Get Copy Number Segmentation Data By Study
get_structural_variants_by_sample | Get Fusions By Sample ID
get_structural_variants_by_study | Get Fusions By Study
get_study_info | Get Metadata on All Available Studies in Database or a Specified Study
impact_gene_info | IMPACT Gene Meta Data
lookup_id | Lookup all available information on what studies a sample ID or patient ID belongs to
set_cbioportal_db | Connect to cBioPortal DB
test_cbioportal_db | Test the Database Connection Anytime During your R Session