Can I download specific types of cancer data?

Yes, the skill allows you to specify data types such as mutations, gene census, structural variants, gene fusions, copy number alterations, and resistance mutations.

Is this skill compatible with standard bioinformatics tools?

Absolutely. Data is downloaded in standard formats like TSV, CSV, and VCF, making it fully compatible with pandas, pysam, bcftools, GATK, and VEP.

How does the skill handle large file downloads?

The provided scripts are optimized for large files, including progress indicators and support for gzip-compressed data to manage COSMIC's multi-gigabyte datasets efficiently.

Does this skill require a COSMIC account?

Yes, users must register at the COSMIC website (cancer.sanger.ac.uk). Academic access is free with registration, while commercial users require a license from QIAGEN.

Which genome assemblies are supported by this skill?

The skill supports both the recommended GRCh38 (current standard) and the legacy GRCh37 assembly for compatibility with older pipelines.

COSMIC Cancer Database Access

Name: COSMIC Cancer Database Access
Author: Microck

byMicrock

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データサイエンスとML

Accesses and downloads comprehensive somatic mutation data from the world's largest cancer genomics database for research and precision oncology.

概要

The COSMIC Database skill enables Claude to programmatically interact with the Catalogue of Somatic Mutations in Cancer, providing seamless access to expert-curated genomic data. It streamlines the retrieval of coding mutations, the Cancer Gene Census, mutational signatures, and structural variants across thousands of cancer types. Designed for bioinformaticians and cancer researchers, this tool simplifies data acquisition pipelines for both GRCh38 and GRCh37 assemblies, allowing for efficient integration of high-quality cancer genomics into analysis workflows and precision medicine research.

主な機能

Integration with pandas and pysam for immediate downstream data analysis
81 GitHub stars
Retrieval of mutational signatures (SBS, DBS, and ID profiles)
Automated downloading of somatic mutation exports and VCF files
Support for both GRCh38 and GRCh37 genome assemblies
Access to the expert-curated Cancer Gene Census for identifying driver genes

ユースケース

Researching drug resistance mutations and clinical annotations in oncology contexts
Filtering variant lists against known cancer-driving genes and somatic mutations
Developing bioinformatics pipelines for mutational signature and fusion gene analysis

概要

主な機能

Integration with pandas and pysam for immediate downstream data analysis
81 GitHub stars
Retrieval of mutational signatures (SBS, DBS, and ID profiles)
Automated downloading of somatic mutation exports and VCF files
Support for both GRCh38 and GRCh37 genome assemblies
Access to the expert-curated Cancer Gene Census for identifying driver genes

ユースケース

Researching drug resistance mutations and clinical annotations in oncology contexts
Filtering variant lists against known cancer-driving genes and somatic mutations
Developing bioinformatics pipelines for mutational signature and fusion gene analysis