Can I use this for drug resistance research?

Yes, the skill provides specific access to COSMIC’s resistance mutation data, which includes clinical annotations regarding drug sensitivity and resistance.

Which genome assemblies are supported?

The skill supports both the recommended GRCh38 assembly and the legacy GRCh37 assembly, allowing for integration with various research pipelines.

Does this skill require a COSMIC account?

Yes, COSMIC requires authentication. 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, and VCF formats. These files are typically provided in gzip-compressed format to handle large datasets efficiently.

How do I handle large file downloads?

The provided scripts include progress tracking for large downloads, and it is recommended to ensure sufficient disk space as some COSMIC datasets can be several gigabytes in size.

COSMIC Cancer Database Integration

Name: COSMIC Cancer Database Integration
Author: Microck

byMicrock

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데이터 과학 및 ML

Access and download somatic mutation data from the COSMIC database for cancer research and bioinformatics pipelines.

The cosmic-database skill enables Claude to programmatically interface with the Catalogue of Somatic Mutations in Cancer (COSMIC), the world's most comprehensive resource for somatic mutation data. It streamlines the process of downloading curated gene lists from the Cancer Gene Census, retrieving mutational signatures, querying gene fusions, and accessing drug resistance data. Ideal for bioinformaticians and oncology researchers, this skill automates the retrieval of large-scale genomic datasets across different assemblies (GRCh38/GRCh37), facilitating seamless integration into data analysis workflows and precision medicine research.

주요 기능

01Automated download of expert-curated Cancer Gene Census (CGC) data

02Integration with Python data science tools like pandas and pysam for immediate analysis

0381 GitHub stars

04Support for mutational signature profiles including SBS, DBS, and ID signatures

05Programmatic access to millions of somatic mutations across thousands of cancer types

06Cross-assembly compatibility for both GRCh38 and GRCh37 genomic data

사용 사례

01Identifying known oncogenes and tumor suppressors for variant filtering in clinical research

02Analyzing mutational signatures to understand underlying mutational processes in specific tumor types

03Building bioinformatics pipelines that require up-to-date cancer mutation datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills cosmic-database

For use in Claude.ai and ChatGPT

Download Skill