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cosmic-database

Fetch COSMIC cancer mutation data via Python script for GRCh38 and GRCh37.

18|1|Updated Dec 27, 2025
Search Tags:#bioinformatics#genomics#mutations#cosmic#data-download#cancer
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill cosmic-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/cosmic-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill cosmic-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

COSMIC hosts comprehensive somatic mutation data; this skill provides programmatic access for cancer genomics researchers to fetch mutation catalogs, gene census, mutational signatures, and related annotations.

Core Features & Use Cases

  • Programmatic access to COSMIC core mutations, Cancer Gene Census, signatures, structural variants, copy number data, and sample information for downstream analyses.
  • Seamless integration into bioinformatics pipelines, with authentication and multiple genome assemblies support (GRCh38/GRCh37).
  • Use Case: Retrieve all coding mutations for a gene of interest and filter by cancer type to prioritize candidates for experimental validation.

Quick Start

Run the download_cosmic script with your COSMIC credentials to fetch the latest mutation data for GRCh38.

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?▼

Download COSMIC cancer mutation data programmatically by running the provided Python script with authenticated COSMIC credentials to fetch core mutations, Cancer Gene Census, and signatures for GRCh38 or GRCh37.

What file formats are supported for exporting COSMIC genomics data?▼

COSMIC genomics data exports support TSV, CSV, and VCF file formats, enabling you to retrieve somatic mutations, structural variants, and copy number data for bioinformatics pipeline integration.

Can I retrieve COSMIC data for both GRCh38 and GRCh37 genome assemblies?▼

Yes, you can retrieve COSMIC data for both GRCh38 and GRCh37 genome assemblies, ensuring access to core mutations, Cancer Gene Census, and mutational signatures across diverse genomics contexts.

Do I need a COSMIC account to fetch cancer gene census and mutational signatures?▼

Yes, authenticated access via COSMIC credentials is required to fetch Cancer Gene Census, mutational signatures, and sample information through the Python script interface.

How do I filter COSMIC coding mutations by cancer type for experimental validation?▼

Retrieve all coding mutations for a gene of interest via the script interface, then filter the resulting TSV or CSV output by cancer type to prioritize candidates for experimental validation.

What COSMIC datasets are available for bioinformatics research workflows?▼

Available COSMIC datasets include core mutations, Cancer Gene Census, mutational signatures, structural variants, copy number data, and sample information for cancer bioinformatics research workflows.

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