cosmic-database

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

1|Updated Jan 14, 2026

Search Tags:#bioinformatics #precision oncology #cancer genomics #cosmic #mutation data #gene census

Ready to run

npx skills add https://github.com/Sologa/codex-pipeline --skill cosmic-database-sologa

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/cosmic-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill cosmic-database-sologa

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 cancer mutation data, gene lists, and signatures for advanced cancer research.

Core Features & Use Cases

Data Download: Download various COSMIC datasets including mutations, gene census, mutational signatures, and structural variants.
Programmatic Access: Integrate COSMIC data into bioinformatics pipelines and research workflows.
Use Case: Researchers can download the Cancer Gene Census to identify known cancer-driving genes and filter their variant data accordingly.

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 for bioinformatics pipelines?▼

This Skill enables programmatic access to the COSMIC database for downloading cancer mutation data, requiring authentication to retrieve datasets in TSV, CSV, and VCF formats for integration into bioinformatics pipelines.

What genomic datasets can I retrieve from the COSMIC database for precision oncology research?▼

You can retrieve cancer mutation data, the Cancer Gene Census, mutational signatures, and structural variants from the COSMIC database to support precision oncology research and identify known cancer-driving genes.

Can I export COSMIC mutation data in VCF format for different genome assemblies?▼

Yes, this Skill supports retrieving COSMIC data in VCF, TSV, and CSV formats for various genome assemblies, ensuring compatibility with your existing cancer genomics analysis workflows.

Do I need authentication credentials to access COSMIC gene census and mutation data?▼

Yes, authentication is required to programmatically access the COSMIC database and download cancer mutation data, gene census, mutational signatures, and structural variants through this Skill.

How do I use the Cancer Gene Census to filter variant data in cancer genomics?▼

Download the Cancer Gene Census file using this Skill to identify known cancer-driving genes, then apply that gene list to filter your variant data within your bioinformatics pipeline for precision oncology analysis.

What Python dependencies are needed to retrieve COSMIC structural variants and mutational signatures?▼

This Skill requires the requests, pandas, and pysam Python libraries to programmatically retrieve COSMIC datasets and process downloaded structural variants and mutational signatures.