Which genome assemblies are supported?

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

COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer.

Does this skill require a subscription?

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

What file formats can I download using this skill?

You can download and process data in several formats, primarily TSV and CSV (often GZIP compressed) and standard VCF for variant analysis.

COSMIC Cancer Mutation Database

Name: COSMIC Cancer Mutation Database
Author: Activer007

byActiver007

0•

Data Science & ML

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

The COSMIC Database skill enables researchers and developers to programmatically access the Catalogue of Somatic Mutations in Cancer, the most comprehensive source for cancer genomics. It provides specialized tools for downloading mutation data, the Cancer Gene Census, mutational signatures, and drug resistance information across various genome assemblies (GRCh38 and GRCh37). This skill simplifies the integration of high-quality cancer mutation data into bioinformatics pipelines, allowing for efficient querying of gene fusions, structural variants, and copy number alterations essential for precision medicine and oncology studies.

Key Features

01Downloadable mutational signature profiles (SBS, DBS, ID) for signature analysis.

020 GitHub stars

03Automated retrieval of drug resistance mutations with clinical annotations.

04Compatibility with both GRCh38 and GRCh37 human genome assemblies.

05Programmatic access to the Cancer Gene Census for curated cancer-related gene lists.

06Support for multiple data formats including TSV, CSV, and VCF files.

Use Cases

01Identifying known cancer genes and their roles as oncogenes or tumor suppressors.

02Integrating COSMIC mutation data into custom bioinformatics and variant annotation pipelines.

03Analyzing mutational signatures to understand underlying mutagenic processes in tumors.

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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