Do I need a COSMIC account to use this skill?

Yes, COSMIC requires authentication. Academic users can register for free at cancer.sanger.ac.uk, while commercial users require a license from QIAGEN.

Can I access specific subsets like drug resistance mutations?

Yes, the skill provides specific shortcuts for downloading drug resistance data, gene fusions, structural variants, and copy number alterations.

What file formats can I download?

You can download data in TSV, CSV, and VCF formats, allowing for easy integration with tools like pandas, bcftools, or GATK.

Which human genome assemblies are supported?

The skill supports both the current GRCh38 (recommended) assembly and the legacy GRCh37 assembly.

COSMIC Cancer Genomics

Name: COSMIC Cancer Genomics
Author: Activer007

byActiver007

0•

Data Science & ML

Accesses and queries the world's largest database of somatic mutations and curated cancer genes for research and precision oncology.

This skill provides programmatic access to the Catalogue of Somatic Mutations in Cancer (COSMIC), the most comprehensive resource for exploring somatic mutations in human cancer. It enables researchers to automate the retrieval of millions of mutations across thousands of cancer types, access the expert-curated Cancer Gene Census, and download specific datasets like mutational signatures or drug resistance profiles. By streamlining the integration of COSMIC data into bioinformatics pipelines, it facilitates high-throughput cancer genomics analysis, clinical annotation, and target gene selection directly within your development environment.

Key Features

010 GitHub stars

02Automated downloading of somatic mutation data in TSV and VCF formats

03Access to the curated Cancer Gene Census for identifying known oncogenes and tumor suppressors

04Retrieval of mutational signature profiles (SBS, DBS, ID) for genomic analysis

05Seamless integration with pandas and pysam for immediate data processing and analysis

06Support for both GRCh38 (modern) and GRCh37 (legacy) human genome assemblies

Use Cases

01Performing mutational signature analysis to understand the etiology of tumor development

02Identifying candidate genes for research using the expert-curated Cancer Gene Census

03Filtering patient genomic variants against known COSMIC mutations for clinical annotation

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills cosmic-database

For use in Claude.ai and ChatGPT

Download Skill