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cosmic-database

Query COSMIC cancer mutation data with authentication and download TSV, VCF, or CSV files.

1|Updated Mar 4, 2026
Search Tags:#genomics#mutations#signatures#census#cosmic#data-download#cancer
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill cosmic-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/cosmic-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill cosmic-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

COSMIC hosts a vast cancer mutation resource; this skill provides a programmable bridge to retrieve mutation data, Cancer Gene Census lists, mutational signatures, gene fusions, copy-number and expression data for cancer research workflows.

Core Features & Use Cases

  • Programmatic data retrieval: download COSMIC core mutations, Cancer Gene Census, mutational signatures, structural variants, copy-number, gene expression, and resistance mutations.
  • Authentication-enabled access: handles user credentials to fetch data securely for academic or commercial use (with appropriate licensing).
  • CLI-friendly data formats: outputs data in TSV/VCF/CSV formats compatible with pandas and standard bioinformatics pipelines.

Quick Start

Use the cosmic-database to download the latest GRCh38 COSMIC mutation dataset, for example CosmicMutantExport.tsv.gz.

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 for genomics research?▼

The script retrieves various COSMIC datasets including core mutations, Cancer Gene Census lists, mutational signatures, structural variants, copy-number, gene expression, and resistance mutations to support comprehensive cancer research workflows.

Can I load COSMIC data directly into Pandas or standard bioinformatics pipelines?▼

Yes, the script outputs data in TSV, VCF, and CSV formats, which are fully compatible with Pandas and standard bioinformatics pipelines for immediate analysis.

Does accessing COSMIC mutation datasets require authentication?▼

Yes, accessing COSMIC mutation datasets requires authentication to securely fetch data for academic or commercial use under appropriate licensing.

Can I retrieve both GRCh38 and GRCh37 COSMIC datasets?▼

Yes, you can retrieve both GRCh38 and GRCh37 COSMIC datasets. The script handles fetching mutation data across these reference genome builds as needed for your research.

What's the best way to get Cancer Gene Census and mutational signatures data programmatically?▼

The best way to programmatically retrieve Cancer Gene Census and mutational signatures data is using this script to query COSMIC, authenticate securely, and download datasets in TSV, VCF, or CSV formats.

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