What data formats can I download?

You can retrieve data in TSV, CSV, and VCF formats, which are easily processed using Python libraries like pandas and pysam.

Which genome assemblies are supported?

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

Can I use this for drug resistance research?

Yes, the skill provides specific functionality to download resistance mutation data with clinical annotations.

Does this skill require a COSMIC account?

Yes, you must register at cancer.sanger.ac.uk. Academic access is free, while commercial users require a license from QIAGEN.

Cosmic Cancer Database Integration

Name: Cosmic Cancer Database Integration
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Accesses and manages somatic mutation data from the COSMIC database for cancer research and precision oncology.

This skill provides a programmatic interface to the Catalogue of Somatic Mutations in Cancer (COSMIC), the world's most comprehensive resource for exploring somatic mutations in human cancer. It enables researchers to automate the retrieval of Cancer Gene Census data, mutational signatures, structural variants, and drug resistance information. By integrating directly into bioinformatics pipelines, it simplifies the process of downloading large-scale genomic datasets, filtering by gene or cancer type, and preparing data for downstream analysis in Python environments using pandas or pysam.

Key Features

01Automated downloading of somatic mutation and Cancer Gene Census data

020 GitHub stars

03Support for both GRCh38 and GRCh37 genome assemblies

04Programmatic filtering of mutations by gene, cancer type, or primary site

05Access to mutational signatures (SBS, DBS, ID) and gene fusions

06Seamless integration with pandas and pysam for immediate data processing

Use Cases

01Identifying known cancer-driving genes using the curated Cancer Gene Census

02Analyzing mutational signatures to understand underlying carcinogenic processes

03Building automated bioinformatics pipelines for variant annotation and clinical research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos cosmic-database

For use in Claude.ai and ChatGPT

Download Skill