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cosmic-database

Query and download somatic mutation data from the COSMIC database.

8|Updated Nov 19, 2025
Search Tags:#bioinformatics#precision oncology#genomics#cancer mutations#data download#cosmic
One-click install
npx skills add https://github.com/sanand0/scientific-research --skill cosmic-database-sanand0
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/cosmic-database
Command: npx skills add https://github.com/sanand0/scientific-research --skill cosmic-database-sanand0

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 COSMIC database, enabling researchers to query and download comprehensive somatic mutation data for cancer research and precision oncology.

Core Features & Use Cases

  • Download Mutation Data: Access detailed somatic mutation information, including point mutations, indels, and genomic annotations.
  • Cancer Gene Census: Retrieve an expert-curated list of genes known to be involved in cancer.
  • Mutational Signatures: Obtain profiles for mutational signature analysis.
  • Structural Variants & Fusions: Query gene fusions and structural rearrangements.
  • Use Case: A researcher needs to identify all known oncogenes with somatic mutations in lung cancer. They can use this Skill to download the Cancer Gene Census and the core mutation data, then filter for relevant genes and tumor types.

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 somatic mutation data from the COSMIC database using Python?▼

To download COSMIC somatic mutation data, use Python scripts leveraging the requests library for API authentication and data retrieval, then process the genomic annotations with pandas and pysam.

What cancer genomics datasets can I retrieve with a COSMIC API query?▼

A COSMIC API query returns the Cancer Gene Census, somatic point mutations, indels, mutational signature profiles, and structural variants to support precision oncology research.

Do I need a user account to access COSMIC cancer mutation data programmatically?▼

Yes, accessing the COSMIC database programmatically requires user authentication to download somatic mutation data, cancer gene census files, and structural variants for academic or commercial cancer research.

Can I use pandas and pysam to filter COSMIC mutations for specific tumor types?▼

Yes, after downloading the core somatic mutation data, you can use pandas to filter genomic annotations for specific genes and tumor types relevant to your cancer genomics research.

How do I get the expert-curated list of known oncogenes from the Cancer Gene Census?▼

You can retrieve the Cancer Gene Census by executing a download script through the cosmic-database skill, providing an expert-curated list of genes known to be involved in cancer for precision oncology analysis.

Is commercial research supported when querying COSMIC mutational signatures?▼

Yes, the COSMIC database supports both academic and commercial research in precision oncology, allowing you to programmatically obtain mutational signature profiles and structural rearrangement data.

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