Do I need an account to use this COSMIC 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 use this skill to study drug resistance?

Yes, the skill provides specific access to COSMIC's resistance mutation data, which includes clinical annotations for drug resistance research.

How often is the COSMIC data updated?

COSMIC is typically updated quarterly. This skill allows you to use the 'latest' tag to always fetch the most recent release or specify a version number for reproducibility.

Which human genome assemblies are supported?

The skill supports both GRCh38 (the current recommended standard) and GRCh37 (legacy) reference genomes.

What file formats can be retrieved using this skill?

You can download data in TSV and CSV formats (typically gzip compressed) for use with pandas, as well as VCF formats for standard variant analysis tools.

COSMIC Cancer Database Access

Name: COSMIC Cancer Database Access
Author: x-cmd

byx-cmd

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Ciencia de Datos y ML

Accesses and queries the Catalogue of Somatic Mutations in Cancer (COSMIC) to retrieve genomic data, mutational signatures, and cancer gene census information.

Acerca de

This skill enables Claude to programmatically interact with the COSMIC database, the world's most comprehensive resource for exploring somatic mutations in human cancer. It facilitates the automated downloading of large-scale genomic datasets, including the Cancer Gene Census, mutational signature profiles, and drug resistance data. Designed for bioinformatics pipelines and precision oncology research, the skill allows users to filter mutations by gene, identify oncogenic roles, and extract variants for specific cancer types across both GRCh37 and GRCh38 genome assemblies while handling authentication and large file downloads seamlessly.

Características Principales

Support for both GRCh37 and GRCh38 human genome assemblies
8 GitHub stars
Querying of structural variants, gene fusions, and copy number alterations
Automated downloading of comprehensive cancer mutation datasets (TSV, CSV, VCF)
Retrieval of SBS, DBS, and ID mutational signature profiles
Access to the expert-curated Cancer Gene Census for identifying driver genes

Casos de Uso

Filtering and analyzing somatic variants for precision oncology and clinical research
Integrating cancer mutation data into automated bioinformatics and data science pipelines
Identifying known cancer genes and their specific roles as oncogenes or tumor suppressors

Acerca de

Características Principales

Support for both GRCh37 and GRCh38 human genome assemblies
8 GitHub stars
Querying of structural variants, gene fusions, and copy number alterations
Automated downloading of comprehensive cancer mutation datasets (TSV, CSV, VCF)
Retrieval of SBS, DBS, and ID mutational signature profiles
Access to the expert-curated Cancer Gene Census for identifying driver genes

Casos de Uso

Filtering and analyzing somatic variants for precision oncology and clinical research
Integrating cancer mutation data into automated bioinformatics and data science pipelines
Identifying known cancer genes and their specific roles as oncogenes or tumor suppressors