cbioportal-database

Name: cbioportal-database
Availability: InStock
Author: OwnLab

Fetch cancer genomics data from the cBioPortal REST API for studies and genes.

21|1|Updated Mar 19, 2026

Search Tags:#bioinformatics #data-analysis #mutation #survival #cancer-genomics #cbioportal #cna

Ready to run

npx skills add https://github.com/OwnLabAI/ownlab --skill cbioportal-database-ownlabai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cbioportal-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/cbioportal-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill cbioportal-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

cBioPortal provides a centralized, programmatic access point to multidimensional cancer genomics data. This skill makes it easy to fetch mutations, copy number alterations, gene expression, and clinical data across hundreds of studies without manual scraping or ad hoc data wrangling.

Core Features & Use Cases

REST API access to studies and molecular profiles, enabling reproducible analyses.
Programmatic retrieval of mutations, CNAs, expression, and clinical attributes for pan-cancer exploration.
Use cases include mutation frequency analysis, survival associations, and cross-study comparisons to validate gene–cancer relationships.

Quick Start

Query brca_tcga_mutations via the API to fetch TP53 mutations and summarize mutation counts.

Frequently Asked Questions about cbioportal-database

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

FAQPage Schema

How do I fetch cancer genomics data like mutations and CNA from cBioPortal?▼

To fetch cancer genomics data from cBioPortal, you query the cBioPortal REST API for specific studies and genes to retrieve structured mutations, CNA, expression, and clinical attributes for downstream analysis.

What is the best way to retrieve TP53 mutation counts for breast cancer studies?▼

Retrieving TP53 mutation counts for breast cancer involves querying a specific study like brca_tcga_mutations via the API to fetch and summarize mutation data without manual scraping or ad hoc data wrangling.

Can I perform survival association analysis using cBioPortal molecular profiles?▼

Yes, you can perform survival association analysis by programmatically retrieving clinical attributes and molecular profiles from cBioPortal to validate gene-cancer relationships across hundreds of studies.

Does programmatic access to cBioPortal support pan-cancer cross-study comparisons?▼

Programmatic access to cBioPortal supports pan-cancer cross-study comparisons by fetching mutations, copy number alterations, and expression data across hundreds of studies for reproducible analyses.

Why does my cBioPortal REST API query for gene expression data fail?▼

Your cBioPortal REST API query for gene expression data may fail due to common API errors; this approach handles these errors with clear guidance and returns structured results to ensure successful data retrieval.