Can I use this for drug resistance research?

Yes, the skill provides specific functionality to access datasets for drug resistance mutations with associated clinical annotations.

Is it possible to filter for specific genes like TP53?

Absolutely. The skill includes patterns and scripts for filtering mutation data by gene name, primary site, or cancer type using Python and pandas.

Which genome assemblies are supported by this skill?

The skill supports both GRCh38 (the current recommendation) and GRCh37 (legacy) assemblies for all data types.

What file formats can I work with?

You can download and process data in several industry-standard formats, including compressed TSV, CSV, and VCF files.

Do I need an account to use the COSMIC skill?

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

COSMIC Cancer Database

Name: COSMIC Cancer Database
Author: Activer007

byActiver007

0•

Data Science & ML

Access and query the world's most comprehensive database of somatic mutations and genomic data for cancer research and precision oncology.

The COSMIC Database skill enables researchers and bioinformaticians to programmatically interact with the Catalogue of Somatic Mutations in Cancer directly within their AI development environment. It streamlines the process of downloading and analyzing extensive datasets, including the Cancer Gene Census, mutational signatures, drug resistance mutations, and structural variants. This skill is essential for integrating high-quality cancer genomics data into bioinformatics pipelines, facilitating tasks like variant annotation, target gene selection, and signature analysis across both GRCh38 and GRCh37 assemblies.

Key Features

01Retrieval of mutational signature profiles including SBS, DBS, and ID signatures

02Automated downloading of comprehensive cancer mutation data and sample metadata

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

040 GitHub stars

05Programmatic analysis of drug resistance mutations and gene fusion events

06Support for multiple genome assemblies (GRCh38/GRCh37) and formats like TSV and VCF

Use Cases

01Analyzing mutational signatures to identify underlying carcinogenic processes

02Researching specific gene mutations and their prevalence across different cancer types

03Building automated bioinformatics pipelines for clinical variant annotation and filtering

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