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cosmic-database

Download cancer genomics data from the COSMIC database using Python scripts.

Updated Mar 10, 2026
Search Tags:#bioinformatics#drug discovery#cancer genomics#cosmic#mutation data#gene census
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill cosmic-database-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/cosmic-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill cosmic-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Catalogue of Somatic Mutations in Cancer (COSMIC), enabling researchers to query and download comprehensive cancer genomics data for analysis.

Core Features & Use Cases

  • Download diverse cancer data: Access mutation data, gene census, mutational signatures, structural variants, copy number alterations, and more.
  • Integrate with bioinformatics pipelines: Use downloaded data for variant annotation, signature analysis, and cancer genomics research.
  • Use Case: Download the COSMIC Cancer Gene Census to identify known cancer-driving genes for targeted therapy research.

Quick Start

Use the cosmic-database skill to download the Cancer Gene Census file.

Frequently Asked Questions about cosmic-database

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

FAQPage Schema
How do I download COSMIC cancer mutation data programmatically?▼

You can download COSMIC mutation data programmatically using Python scripts that leverage the requests library. This facilitates automated retrieval of comprehensive cancer genomics datasets for research pipelines.

Do I need to authenticate to access the COSMIC database for cancer genomics research?▼

Yes, accessing the COSMIC database requires authentication. You must configure your Python scripts with valid credentials to successfully download mutation data, gene census, and structural variants.

Can I use pandas and pysam to integrate COSMIC data into bioinformatics pipelines?▼

Yes, this Skill relies on pandas and pysam dependencies, allowing you to parse and integrate downloaded COSMIC mutation data directly into existing bioinformatics pipelines for variant annotation.

What specific cancer genomics data can I retrieve from the COSMIC database?▼

You can retrieve mutation data, the Cancer Gene Census, mutational signatures, structural variants, and copy number alterations. These datasets directly support drug discovery and precision oncology research.

What is the best way to identify known cancer-driving genes for targeted therapy research?▼

The best way is to download the COSMIC Cancer Gene Census file using these Python scripts. It provides a comprehensive list of known cancer-driving genes for targeted therapy research.

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