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 require a license from QIAGEN.

Which genome assemblies are supported by this skill?

The skill supports both the current GRCh38 standard and the legacy GRCh37 (hg19) assembly, allowing for compatibility with various bioinformatics pipelines.

Can this skill handle large genomic datasets?

Yes, it includes specialized scripts designed to handle multi-gigabyte file downloads with progress tracking and supports compressed formats like .gz and .vcf.

What kind of cancer data can I retrieve?

You can access somatic mutations, the Cancer Gene Census, mutational signatures, gene fusions, structural variants, drug resistance mutations, and copy number alterations.

Cosmic Cancer Mutation Database

Name: Cosmic Cancer Mutation Database
Author: Activer007

byActiver007

0•

データサイエンスとML

Accesses and integrates the world's largest somatic mutation database for cancer genomics and precision oncology research.

The COSMIC Database skill enables researchers and bioinformaticians to programmatically interact with the Catalogue of Somatic Mutations in Cancer. It simplifies the retrieval of extensive cancer genomics data, including curated gene lists from the Cancer Gene Census, mutational signatures, and structural variants across thousands of cancer types. Designed for seamless integration into bioinformatics pipelines, this skill facilitates the study of drug resistance, gene fusions, and copy number alterations, providing a standardized way to download and process high-quality cancer mutation data for both academic and clinical research purposes.

主な機能

01Automated downloading of somatic mutation data and VCF files

02Retrieval of mutational signature profiles (SBS, DBS, and ID)

03Support for both GRCh38 and GRCh37 genome assemblies

04Access to structural variants, gene fusions, and resistance mutations

05Programmatic access to the expert-curated Cancer Gene Census

060 GitHub stars

ユースケース

01Filtering variant call files against known cancer-driving mutations for clinical annotation

02Analyzing mutational signatures to understand underlying cancer mutational processes

03Identifying oncogenic roles and tumor suppressor genes for research target selection

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

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