Browse and Query Clinical and Genomic Data from cBioPortal
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Documentation for package ‘cbioportalR’ version 1.1.0
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 |
| set_cbioportal_db | Connect to cBioPortal DB |
| test_cbioportal_db | Test the Database Connection Anytime During your R Session |