Is a COSMIC account required to use this skill?

Yes, COSMIC requires authentication. Academic users can register for free on the COSMIC website, while commercial users require a license from QIAGEN.

Which genome assemblies does the skill support?

It supports both GRCh37 (legacy) and GRCh38 (current standard) reference genomes, allowing you to specify the assembly in your data requests.

What file formats are supported?

The skill facilitates the retrieval of standard bioinformatics formats including TSV and CSV for tabular data, and VCF for variant-specific information.

How often is the COSMIC data updated?

COSMIC is typically updated quarterly. This skill allows you to use the 'latest' keyword in file paths to ensure you are always retrieving the most recent release.

Can I download data for specific cancer types?

Yes, you can download comprehensive mutation files and then use the provided Python examples to filter data by primary site or cancer type using pandas.

COSMIC Cancer Mutation Database

Name: COSMIC Cancer Mutation Database
Author: Microck

byMicrock

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データサイエンスとML

Accesses and queries the world's most comprehensive database of somatic mutations for cancer research and precision oncology.

This skill provides a streamlined interface for interacting with the Catalogue of Somatic Mutations in Cancer (COSMIC), the premier resource for exploring human cancer genomics. It enables researchers and bioinformaticians to programmatically download curated datasets, including the Cancer Gene Census, mutational signatures, structural variants, and drug resistance data. By facilitating the integration of high-quality somatic mutation data directly into bioinformatics pipelines, it simplifies the process of filtering variants, identifying oncogenes, and conducting large-scale genomic analysis across various cancer types and reference assemblies.

主な機能

01Access to mutational signatures (SBS, DBS, ID) and structural variants

02Programmatic download of somatic mutation data and the Cancer Gene Census

03Support for both GRCh37 and GRCh38 genome assemblies

0489 GitHub stars

05Integration with Python data science tools like pandas and pysam for immediate analysis

06Automated retrieval of drug resistance mutations and clinical annotations

ユースケース

01Filtering experimental sequencing data against known cancer mutations and gene lists

02Extracting mutational signature profiles for large-scale tumor characterization projects

03Building automated bioinformatics pipelines for precision oncology and drug resistance research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills cosmic-database

For use in Claude.ai and ChatGPT

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