Can I use this for drug resistance research?

Yes, the skill includes specific functionality to download and analyze drug resistance mutations with clinical annotations for cancer research.

What file formats can the skill handle?

It manages TSV, CSV, and VCF files, which are the standard formats for COSMIC data and can be processed using libraries like pandas or pysam.

Is this skill part of the Kosmos AI Scientist project?

Yes, this skill is a specialized component of the Kosmos implementation, designed to enable Claude to act as an AI scientist for autonomous cancer research.

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.

Which genome assemblies are supported by this skill?

The skill supports both GRCh38 (the current standard) and GRCh37 (legacy) reference genomes to ensure compatibility with various research pipelines.

COSMIC Cancer Database Access

Name: COSMIC Cancer Database Access
Author: jimmc414

byjimmc414

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324

データサイエンスとML

Accesses and integrates the world's most comprehensive database for exploring somatic mutations in human cancer into bioinformatics workflows.

概要

The cosmic-database skill enables Claude to programmatically interact with the Catalogue of Somatic Mutations in Cancer (COSMIC), the premier resource for cancer genomics research. It provides tools for downloading and analyzing a vast array of data, including somatic mutations, curated gene lists from the Cancer Gene Census, mutational signatures, and structural variants. Designed for precision oncology and bioinformatics, it simplifies the process of fetching large datasets and integrating them into Python-based analysis pipelines, supporting both GRCh38 and GRCh37 genome assemblies for autonomous scientific discovery.

主な機能

324 GitHub stars
Support for structural variants, gene fusions, and copy number alterations
Access to the expert-curated Cancer Gene Census list
Automated downloading of somatic mutation data and sample metadata
Seamless integration with pandas and pysam for bioinformatics analysis
Retrieval of mutational signature profiles including SBS, DBS, and ID

ユースケース

Integrating COSMIC data into large-scale bioinformatics pipelines and AI discovery workflows
Filtering genomic variants by their known clinical relevance in cancer research
Automating the retrieval of drug resistance mutation data for precision medicine

概要

主な機能

324 GitHub stars
Support for structural variants, gene fusions, and copy number alterations
Access to the expert-curated Cancer Gene Census list
Automated downloading of somatic mutation data and sample metadata
Seamless integration with pandas and pysam for bioinformatics analysis
Retrieval of mutational signature profiles including SBS, DBS, and ID

ユースケース

Integrating COSMIC data into large-scale bioinformatics pipelines and AI discovery workflows
Filtering genomic variants by their known clinical relevance in cancer research
Automating the retrieval of drug resistance mutation data for precision medicine