Can this skill help with mutational signature analysis?

Yes, it provides programmatic access to SBS, DBS, and ID signature definitions used in mutational signature decomposition and analysis.

Is a COSMIC account required to use this skill?

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

What file formats can I download using this skill?

You can download data in TSV/CSV formats for easy processing with pandas, or VCF format for standard variant analysis tools like bcftools.

How do I ensure I am using the most recent COSMIC data?

By using the 'latest' tag in your queries, the skill automatically retrieves data from the most recent quarterly COSMIC release.

Which genome assemblies are supported?

The skill supports both GRCh38 (current standard) and GRCh37 (legacy) reference genomes to match your specific pipeline needs.

COSMIC Cancer Database Access

Name: COSMIC Cancer Database Access
Author: henriquescastilho

byhenriquescastilho

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Data Science & ML

Accesses the world's largest database of somatic mutations in cancer to retrieve genomic data, gene census lists, and mutational signatures.

The COSMIC Database skill enables researchers and developers to programmatically interact with the Catalogue of Somatic Mutations in Cancer. It facilitates the automated download and analysis of comprehensive cancer genomics data, including curated gene lists from the Cancer Gene Census, mutational signature profiles, and structural variant data. This skill is ideal for building bioinformatics pipelines, performing precision oncology research, and managing clinical annotation workflows, providing a structured and efficient way to integrate high-quality somatic mutation data directly into your computational environment.

Key Features

01Query structural variants, gene fusions, and copy number alterations

02Support for both GRCh37 and GRCh38 human genome assemblies

031 GitHub stars

04Download comprehensive cancer mutation data in TSV or VCF formats

05Retrieve mutational signature profiles for genomic analysis

06Access the expert-curated Cancer Gene Census for identifying key oncogenes

Use Cases

01Integrating somatic mutation data into automated bioinformatics pipelines

02Filtering variant call files (VCFs) against known cancer-driving mutations

03Identifying drug resistance mutations and gene roles for precision medicine research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add henriquescastilho/my-claude cosmic-database

For use in Claude.ai and ChatGPT

Key Features

01Query structural variants, gene fusions, and copy number alterations

02Support for both GRCh37 and GRCh38 human genome assemblies

031 GitHub stars

04Download comprehensive cancer mutation data in TSV or VCF formats

05Retrieve mutational signature profiles for genomic analysis

06Access the expert-curated Cancer Gene Census for identifying key oncogenes

Use Cases

01Integrating somatic mutation data into automated bioinformatics pipelines

02Filtering variant call files (VCFs) against known cancer-driving mutations

03Identifying drug resistance mutations and gene roles for precision medicine research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add henriquescastilho/my-claude cosmic-database

For use in Claude.ai and ChatGPT