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cbioportal-database

Query cBioPortal REST API for cancer genomics data and survival correlations.

Updated Mar 10, 2026
Search Tags:#cancer genomics#survival analysis#gene expression#cbioportal#copy number alteration#mutation analysis
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill cbioportal-database-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cbioportal-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/cbioportal-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill cbioportal-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to vast cancer genomics datasets, enabling researchers to quickly find and analyze mutations, copy number alterations, and expression data across numerous cancer studies.

Core Features & Use Cases

  • Data Exploration: Query specific genes for mutation frequencies, copy number status, and expression levels within defined cancer types.
  • Survival Analysis: Correlate genomic alterations with patient survival outcomes.
  • Pan-Cancer Analysis: Compare alteration patterns across multiple cancer studies.
  • Use Case: Investigate the mutation frequency of the TP53 gene in breast cancer (BRCA) and its correlation with overall survival.

Quick Start

Use the cbioportal-database skill to find 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 for mutation frequencies and copy number alterations across multiple studies?▼

To query cancer genomics data for mutation frequencies and copy number alterations, this Skill integrates with the cBioPortal REST API to retrieve somatic mutations and expression data across diverse cancer studies.

Can I perform survival analysis by correlating gene expression with patient outcomes in specific cancer types?▼

Yes, you can perform survival analysis by correlating genomic alterations like gene expression with patient survival outcomes within defined cancer types using data fetched from the cBioPortal API.

What is the best way to compare pan-cancer alteration patterns for oncogenes and tumor suppressors?▼

The best way to compare pan-cancer alteration patterns for oncogenes and tumor suppressors is to programmatically query the cBioPortal database to analyze alteration frequencies across multiple cancer studies.

Does this Skill require pandas and requests to retrieve cancer genomics data from the cBioPortal API?▼

Yes, this Skill requires the requests and pandas dependencies to programmatically interface with the cBioPortal REST API and structure the retrieved cancer genomics data for analysis.

How do I find the mutation frequency of a specific gene like TP53 in the BRCA TCGA study?▼

You can find the TP53 mutation frequency in the BRCA TCGA study by using this Skill to query the cBioPortal database for somatic mutation data within that specific cancer study.

Can I use this Skill to investigate both gene expression levels and copy number status for targeted cancer research?▼

Yes, you can use this Skill to investigate gene expression levels and copy number status for targeted cancer research by querying the cBioPortal database for comprehensive genomic profiles across diverse cancer studies.

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