Which genome assemblies are supported by this skill?

The skill supports both the recommended current standard, GRCh38, and the legacy GRCh37 assembly for compatibility with older pipelines.

How are large genomic files handled?

The integrated scripts manage large file downloads (often several GB) with progress tracking. Users should ensure they have sufficient disk space before initiating full database exports.

What types of cancer data can I download?

You can download a wide range of data including coding mutations, the Cancer Gene Census, mutational signatures, gene fusions, copy number alterations, and drug resistance mutations.

Do I need an account to use the COSMIC database skill?

Yes, COSMIC requires authentication. Academic users can register for free at the Sanger Institute website, while commercial users must obtain a license from QIAGEN.

COSMIC Cancer Genomics

Name: COSMIC Cancer Genomics
Author: plurigrid

byplurigrid

•

Data Science & ML

Integrates the COSMIC cancer mutation database into bioinformatics workflows for somatic mutation analysis and precision oncology research.

The COSMIC (Catalogue of Somatic Mutations in Cancer) Database skill provides programmatic access to the world's most comprehensive resource for exploring somatic mutations in human cancer. It streamlines the retrieval of curated datasets, including the Cancer Gene Census, mutational signatures, and complex genomic variants like fusions and copy number alterations. By automating authentication and file management, this skill allows researchers and bioinformaticians to efficiently integrate high-quality cancer genomics data into their computational pipelines for variant filtering, drug resistance studies, and tumor profiling.

Key Features

018 GitHub stars

02Access to comprehensive mutational signature profiles (SBS, DBS, and ID signatures)

03Cross-assembly support for both GRCh38 (current) and GRCh37 (legacy) reference genomes

04Automated downloading of somatic mutation data and the expert-curated Cancer Gene Census

05Retrieval of specialized datasets for structural variants, gene fusions, and drug resistance

06Support for multiple data formats including TSV, CSV, and VCF for seamless tool integration

Use Cases

01Extracting mutational signature data for tumor mutational burden and signature decomposition analysis

02Filtering clinical sequencing results against known cancer-driving mutations and curated gene lists

03Building automated bioinformatics pipelines that stay synchronized with the latest quarterly COSMIC releases

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add plurigrid/asi cosmic-database

For use in Claude.ai and ChatGPT

Download Skill