Can I filter mutations by specific genes?

Yes, the skill provides helper functions and patterns to filter large mutation datasets by gene name, cancer type, or role in cancer (e.g., oncogene vs. tumor suppressor).

Which genome assemblies does this skill support?

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

Does this skill require authentication?

Yes, users must register for an account at cancer.sanger.ac.uk. Academic use is free, while commercial users require a license from QIAGEN.

What data formats are available through this skill?

You can access data in several formats, including TSV, CSV, and VCF, which can be processed using libraries like pandas and pysam.

What is the COSMIC Database skill used for?

This skill is used to programmatically download and query cancer genomics data from the Catalogue of Somatic Mutations in Cancer for research and clinical analysis.

COSMIC Cancer Mutation Database

Name: COSMIC Cancer Mutation Database
Author: Yezez9

byYezez9

0•

Data Science & ML

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

The COSMIC Database skill provides programmatic access to the Catalogue of Somatic Mutations in Cancer, the most comprehensive global resource for exploring human cancer genomics. It enables researchers and bioinformaticians to automate the retrieval of millions of mutations, expert-curated gene lists from the Cancer Gene Census, and complex mutational signatures. By facilitating the download and processing of TSV, CSV, and VCF files across both GRCh37 and GRCh38 assemblies, this skill streamlines the integration of high-quality genomic data into automated bioinformatics pipelines and precision medicine research workflows.

Key Features

010 GitHub stars

02Access to the expert-curated Cancer Gene Census for identifying known cancer drivers

03Automated querying of drug resistance mutations and gene fusion events

04Support for both GRCh38 and GRCh37 reference genome assemblies

05Programmatic download of comprehensive somatic mutation data and sample metadata

06Retrieval of mutational signature profiles including SBS, DBS, and ID signatures

Use Cases

01Building automated bioinformatics pipelines for variant annotation and filtering

02Integrating clinical drug resistance data into oncology research and reports

03Conducting large-scale research on mutational signatures across different cancer types

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent cosmic-database

For use in Claude.ai and ChatGPT

Key Features

010 GitHub stars

02Access to the expert-curated Cancer Gene Census for identifying known cancer drivers

03Automated querying of drug resistance mutations and gene fusion events

04Support for both GRCh38 and GRCh37 reference genome assemblies

05Programmatic download of comprehensive somatic mutation data and sample metadata

06Retrieval of mutational signature profiles including SBS, DBS, and ID signatures

Use Cases

01Building automated bioinformatics pipelines for variant annotation and filtering

02Integrating clinical drug resistance data into oncology research and reports

03Conducting large-scale research on mutational signatures across different cancer types