cbioportal-database

# cBioPortal Database ## Overview cBioPortal for Cancer Genomics is a public repository of cancer genomics data including TCGA, ICGC, and hundreds of curated studies spanning 100+ cancer types. It provides somatic mutation profiles, copy number alterations (CNA), gene expression, clinical data (survival, stage, treatment history), and methylation data for tens of thousands of patient samples. Data is accessible via a REST API at `https://www.cbioportal.org/api/` with no authentication required. ## When to Use - Retrieving somatic mutation profiles (variant type, amino acid change) for a gene across TCGA studies - Querying copy number alteration data (amplification, deep deletion) for candidate cancer driver genes - Accessing clinical data — overall survival, disease-free survival, tumor stage — for survival curve analysis - Identifying which cancer studies have molecular profiling data for a specific cancer type (e.g., breast, lung) - Downloading gene expression (RNA-seq FPKM/RSEM) data from specific TCGA cohorts for differential expression analysis - Correlating genomic alterations with clinical outcomes in a specific study - Use `gnomad-database` instead when you need population-level variant allele frequencies in healthy individuals - For drug-gene interaction lookups use `opentargets-database`; cBioPortal provides the genomic alteration data, not drug interaction annotations ## Prerequisites - **Python packages**: `requests`, `pandas`, `matplotlib` - **Data requirem...