Do I need an account to use this skill?

Yes, COSMIC requires registration for data access. Academic users can register for free at the COSMIC website, while commercial users require a license from QIAGEN.

Can I automate the filtering of mutations by gene name?

Yes, the skill provides patterns for using Python and pandas to filter downloaded mutation sets by gene name, primary site, or specific cancer roles.

Does this skill provide drug resistance data?

Yes, it allows you to specifically download and query the CosmicResistanceMutations dataset which includes clinical annotations for drug resistance.

Which genome assemblies are supported by this skill?

The skill supports both the current standard GRCh38 assembly and the legacy GRCh37 reference genome for historical data comparisons.

What data formats are available for download?

The skill retrieves data in standard bioinformatics formats including TSV, CSV, and VCF, making it compatible with tools like pandas, pysam, and GATK.

COSMIC Cancer Genomics Database

Name: COSMIC Cancer Genomics Database
Author: oimiragieo

byoimiragieo

•

Data Science & ML

Provides programmatic access to the world's largest database of somatic mutations for cancer research and precision oncology.

The COSMIC Database skill streamlines the integration of the Catalogue of Somatic Mutations in Cancer into bioinformatics workflows. It enables researchers to programmatically download and query extensive datasets, including the Cancer Gene Census, mutational signatures, structural variants, and drug resistance data. By automating the authentication and retrieval process, this skill facilitates deep genomic analysis, variant annotation, and target gene selection, making it an essential tool for oncology-focused data science and clinical research.

Key Features

01Retrieval of Single Base Substitution (SBS) and doublet mutational signatures

02Automated downloading of COSMIC mutation data in TSV and VCF formats

03Support for both GRCh38 and GRCh37 genome assemblies

04Direct access to the expert-curated Cancer Gene Census for identifying drivers

0512 GitHub stars

06Querying of gene fusions, copy number alterations, and structural variants

Use Cases

01Building automated bioinformatics pipelines for precision oncology and drug resistance research

02Analyzing mutational signatures to understand underlying carcinogenic processes

03Filtering patient variants against known cancer-driving mutations and gene lists

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add oimiragieo/agent-studio cosmic-database

For use in Claude.ai and ChatGPT

Download Skill