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db-cbioportal

Query cBioPortal REST API for cancer genomics data using Python requests and pandas.

Updated Mar 13, 2026
Search Tags:#cancer genomics#survival analysis#cbioportal#mutation data#genomic data#copy number alteration
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-cbioportal
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-cbioportal
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-cbioportal
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-cbioportal

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 query mutations, copy number alterations, and clinical data across numerous cancer studies.

Core Features & Use Cases

  • Data Exploration: Investigate mutation frequencies, co-occurrence patterns, and alteration profiles for specific genes.
  • Survival Analysis: Correlate genomic alterations with patient survival outcomes.
  • Pan-Cancer Analysis: Compare genomic landscapes across different cancer types.
  • Use Case: Determine the mutation frequency of the TP53 gene in breast cancer (BRCA_TCGA) and compare it to its frequency in lung adenocarcinoma (LUAD_TCGA).

Quick Start

Use the db-cbioportal skill to get the mutation frequency of TP53 in the BRCA_TCGA study.

Frequently Asked Questions about db-cbioportal

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

FAQPage Schema
How do I query cancer genomics data for somatic mutations and clinical patient information?▼

This Skill queries cancer genomics data via the cBioPortal REST API to retrieve somatic mutations, copy number alterations, and clinical patient information across hundreds of cancer studies using Python requests and pandas.

Can I compare mutation frequencies of a specific gene across different cancer studies?▼

Yes, querying cBioPortal via this Skill enables pan-cancer analysis, allowing you to compare mutation frequencies and genomic alteration profiles across different cancer studies like BRCA_TCGA and LUAD_TCGA.

Does this Skill support survival analysis for patients with specific genomic alterations?▼

Yes, it supports survival analysis by allowing you to correlate specific genomic alterations with patient survival outcomes using clinical data retrieved from cBioPortal studies via the REST API.

What do I need to analyze cBioPortal mutation data using Python?▼

To analyze cBioPortal mutation data, you need a Python environment with the requests and pandas libraries installed to query the REST API and structure the returned cancer genomics data for analysis.

How does querying cBioPortal via REST API compare to downloading raw genomic data files?▼

Querying cBioPortal via the REST API provides targeted, programmatic access to specific mutation and copy number alteration data across studies, avoiding the need to manually download and parse massive raw genomic data files.

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