Do I need an account to use the COSMIC database skill?

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

Can I filter mutations by specific genes using this skill?

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

Which genome assemblies are supported?

The skill supports both the current standard GRCh38 assembly and the legacy GRCh37 assembly for older pipelines.

What file formats does this skill handle?

The skill supports TSV and CSV formats for tabular data, as well as VCF formats for genomic variants, typically in compressed .gz format.

COSMIC Cancer Database Access

Name: COSMIC Cancer Database Access
Author: jackspace

byjackspace

•

Data Science & ML

Accesses and retrieves extensive cancer genomics data from the COSMIC database for bioinformatics and precision oncology research.

This skill provides programmatic access to the Catalogue of Somatic Mutations in Cancer (COSMIC), the world's most comprehensive resource for exploring somatic mutations. It enables researchers and bioinformaticians to automate the downloading and processing of curated gene lists, mutational signatures, gene fusions, and drug resistance data. By streamlining the integration of cancer genomics into data science pipelines, this skill facilitates deep analysis of mutations across thousands of cancer types using both GRCh38 and GRCh37 assemblies.

Key Features

01Retrieval of specialized datasets like mutational signatures and resistance data

022 GitHub stars

03Programmatic download of somatic mutation data and the Cancer Gene Census

04Support for multiple genome assemblies including GRCh38 and GRCh37

05Seamless integration with pandas and pysam for immediate data analysis

06Command-line and script-based access for batch data processing

Use Cases

01Identifying drug resistance mutations to support precision oncology research

02Filtering clinical variants against the expert-curated Cancer Gene Census

03Automating the retrieval of mutational signatures for tumor profile analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jackspace/claudeskillz scientific-db-cosmic-database

For use in Claude.ai and ChatGPT

Download Skill