cbioportal-database

Query cBioPortal REST API for cancer genomics data using Python.

Updated Mar 10, 2026

Search Tags:#cancer genomics #survival analysis #gene expression #cbioportal #mutation data #copy number alteration

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill cbioportal-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cbioportal-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/cbioportal-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill cbioportal-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to a vast repository of cancer genomics data, enabling researchers to analyze mutations, copy number alterations, and gene expression across hundreds of cancer studies.

Core Features & Use Cases

Query cBioPortal: Access somatic mutations, copy number alterations (CNA), gene expression, and survival data.
Cancer Genomics Analysis: Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.
Use Case: Investigate the mutation frequency of a specific gene across multiple TCGA cancer types to identify potential pan-cancer targets.

Quick Start

Use the cbioportal-database skill to get the mutation frequency of TP53 in the brca_tcga study.

Frequently Asked Questions about cbioportal-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I query cancer genomics data from cBioPortal using Python?▼

You can query cBioPortal cancer genomics data using Python by leveraging the requests library to call the REST API, retrieving somatic mutations and gene expression for analysis with pandas.

What is the best way to analyze mutation frequency across multiple TCGA cancer studies?▼

Analyze mutation frequency across TCGA cancer studies by querying the cBioPortal API for somatic mutations, then process the returned data with pandas to calculate pan-cancer target frequencies.

Can I retrieve patient survival data and gene expression from cBioPortal for analysis?▼

Yes, you can retrieve patient survival data and gene expression from cBioPortal. The Skill queries the REST API to fetch these datasets, enabling patient-level genomic profiling and survival analysis.

Does this cBioPortal query approach require pandas and requests dependencies?▼

Yes, querying cBioPortal requires the pandas and requests dependencies. Requests handles REST API data retrieval, while pandas structures and analyzes the returned cancer genomics datasets.

How do I validate oncogenes and tumor suppressors using copy number alteration data?▼

Validate oncogenes and tumor suppressors by querying cBioPortal for copy number alteration data, then using pandas to analyze CNA frequencies across patient cohorts and identify significant genomic patterns.