Which genome assemblies are supported by this skill?

The skill supports both GRCh38 (the current recommended standard) and GRCh37 (legacy) assemblies for all major data types.

How does this skill handle large file downloads?

The included scripts provide progress tracking for large files, which can often be several gigabytes in size, ensuring reliable data retrieval for comprehensive datasets.

What Python dependencies are required?

To use the downloaded data effectively, you should have 'requests' and 'pandas' installed, and 'pysam' if you plan on working with VCF files.

Do I need an account to use the COSMIC database skill?

Yes, COSMIC requires authentication. Academic users can register for free at the COSMIC website, while commercial users require a license through QIAGEN.

Can I download specific data types like mutational signatures?

Yes, the skill provides specific shorthand and helper functions to download mutational signatures, gene fusions, resistance mutations, and the Cancer Gene Census.

COSMIC Cancer Database

Name: COSMIC Cancer Database
Author: Microck

byMicrock

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Ciencia de Datos y ML

Accesses the Catalogue of Somatic Mutations in Cancer (COSMIC) to retrieve somatic mutations, gene fusions, and mutational signatures for oncology research.

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The COSMIC Cancer Database skill provides a programmatic interface for interacting with the world's most comprehensive resource for somatic mutations in human cancer. It enables bioinformaticians and researchers to download curated datasets including the Cancer Gene Census, mutational signature profiles, and structural variants directly into their analysis pipelines. By automating the retrieval of high-quality genomic data and supporting both GRCh37 and GRCh38 assemblies, this skill streamlines precision oncology workflows and facilitates the integration of clinical annotations into cancer research projects.

Características Principales

Querying of structural variants, gene fusions, and copy number alterations
Built-in support for both legacy GRCh37 and modern GRCh38 genome assemblies
Automated retrieval of somatic mutation datasets in TSV and VCF formats
Access to the expert-curated Cancer Gene Census for identifying driver genes
81 GitHub stars
Download of mutational signature profiles including SBS, DBS, and ID signatures

Casos de Uso

Researching drug resistance mutations and clinical annotations for precision medicine
Integrating comprehensive cancer mutation data into automated bioinformatics pipelines
Filtering genomic variants against known cancer signatures and curated gene lists

Acerca de

Características Principales

Querying of structural variants, gene fusions, and copy number alterations
Built-in support for both legacy GRCh37 and modern GRCh38 genome assemblies
Automated retrieval of somatic mutation datasets in TSV and VCF formats
Access to the expert-curated Cancer Gene Census for identifying driver genes
81 GitHub stars
Download of mutational signature profiles including SBS, DBS, and ID signatures

Casos de Uso

Researching drug resistance mutations and clinical annotations for precision medicine
Integrating comprehensive cancer mutation data into automated bioinformatics pipelines
Filtering genomic variants against known cancer signatures and curated gene lists