cosmic-database

Query and download COSMIC cancer mutation data in TSV, CSV, and VCF formats.

Updated Dec 17, 2025

Search Tags:#bioinformatics #precision oncology #cosmic #mutation analysis #cancer mutation

Ready to run

npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill cosmic-database-robotlearning123

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/cosmic-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill cosmic-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

The Cosmic Database Skill Unit simplifies access to the COSMIC cancer mutation database, enabling users to query somatic mutations, gene lists, mutational signatures, and more, directly within their research workflows.

Core Features & Use Cases

COSMIC Data Access: Access comprehensive cancer genomics data including mutations, gene lists, and mutational signatures.
Data Download: Download mutation data in TSV, CSV, and VCF formats.
Use Case: Researchers can use this Skill to download cancer mutation data for specific genes, cancer types, or genome assemblies, and integrate it into their bioinformatics pipelines.

Quick Start

Use the cosmic-database skill to download mutation data for the gene TP53 from the GRCh38 genome assembly.

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 for specific genes in my bioinformatics pipeline?▼

You can download COSMIC cancer mutation data for specific genes by querying the database directly within your research workflows using this Skill. It enables retrieving somatic mutations, gene lists, and structural variants for targeted bioinformatics analysis.

What file formats are supported for exporting somatic mutation data from the COSMIC database?▼

Somatic mutation data from the COSMIC database can be downloaded in TSV, CSV, and VCF formats. These formats facilitate integration into various precision oncology research pipelines.

Do I need pysam and pandas installed to retrieve COSMIC mutational signatures?▼

Yes, retrieving and processing COSMIC mutational signatures requires Python with requests, pandas, and pysam libraries installed. These dependencies handle data retrieval and processing for mutation analysis.

Can I query structural variants and genome assemblies like GRCh38 using this COSMIC integration?▼

Yes, you can query structural variants and download mutation data for specific genome assemblies like GRCh38 using this COSMIC integration. It supports filtering by cancer types and genome assemblies for precision oncology research.

What is the best way to integrate COSMIC somatic mutation data into precision oncology workflows?▼

The best way to integrate COSMIC somatic mutation data into precision oncology workflows is by using a programmatic Skill to query and download gene lists and mutational signatures. This approach embeds comprehensive cancer genomics data directly into your analysis pipelines.