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alterlab-cbioportal

Query cBioPortal API for gene mutations and copy-number alterations across cancer studies.

58|9|Updated Mar 16, 2026
Search Tags:#data-analysis#mutations#cancer-genomics#clinical-data#cbioportal#copy-number#pan-cancer
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cbioportal
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-cbioportal
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-cbioportal
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cbioportal

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill enables researchers to programmatically access multidimensional cancer genomics data from cBioPortal, enabling rapid querying of mutations, CNAs, expression, and clinical associations across hundreds of studies.

Core Features & Use Cases

  • REST API access to studies, molecular profiles, mutations, CNAs, expression, and clinical data.
  • Examples and workflows for retrieving gene-level mutation data, altering frequency, and survival associations.
  • Pan-cancer analyses across TCGA, GENIE, and MSK-IMPACT to compare alteration patterns and clinical correlations.

Quick Start

Query the cBioPortal REST API for a gene across a study and summarize mutation and CNA counts.

Frequently Asked Questions about alterlab-cbioportal

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

FAQPage Schema
How do I query cBioPortal for mutation and copy-number alteration frequencies?▼

Retrieve mutation and copy-number alteration frequencies by querying the cBioPortal REST API with Entrez gene IDs via the /genes/fetch endpoint and molecular data endpoints to identify patient-level patterns within a cancer study.

Can I perform pan-cancer analyses across TCGA and GENIE studies?▼

Yes, you can perform pan-cancer analyses across TCGA, GENIE, and MSK-IMPACT studies to compare alteration patterns, evaluate mutation frequencies, and identify clinical or survival associations across cohorts.

What do I need to retrieve gene-level mutation data from cBioPortal?▼

You need the target gene's Entrez gene ID to access molecular data endpoints, which return patient-level mutation counts, CNA data, and clinical associations for the specified cancer study.

Does the cBioPortal API support retrieving clinical and survival associations?▼

Yes, the cBioPortal REST API provides clinical data endpoints to evaluate survival associations and clinical correlations alongside mutation and CNA data for cross-study comparisons.

How does the skill handle missing data in cBioPortal molecular profiles?▼

The skill includes appropriate handling for missing data when querying molecular profiles, ensuring mutation frequencies and copy-number alteration counts are accurately summarized despite incomplete datasets.

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