Can I filter downloaded data by specific genes like TP53?

Yes, the skill provides implementation patterns using pandas to filter mutation files by gene name, primary site, or functional role in cancer.

Which genome assemblies are supported by the COSMIC skill?

The skill supports both the current GRCh38 standard and the legacy GRCh37 reference genomes for all mutation data downloads.

Does this skill require a COSMIC account?

Yes, authentication is required. Academic users can register for free at cancer.sanger.ac.uk, while commercial users require a license from QIAGEN.

What file formats does the COSMIC skill handle?

The skill can retrieve and process data in several standard formats including TSV, CSV, and VCF (Variant Call Format) for compatibility with tools like GATK or bcftools.

COSMIC Cancer Genomics Access

Name: COSMIC Cancer Genomics Access
Author: Microck

byMicrock

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데이터 과학 및 ML

Access and query the world's largest database of somatic mutations and cancer genomics data for precision oncology research.

소개

This skill enables Claude to programmatically interact with the COSMIC (Catalogue of Somatic Mutations in Cancer) database, allowing researchers and bioinformaticians to automate the retrieval of high-quality cancer mutation data. It facilitates the downloading of curated datasets such as the Cancer Gene Census, mutational signatures, and drug resistance profiles, while streamlining the integration of these findings into Python-based bioinformatics pipelines for both GRCh38 and GRCh37 genome assemblies.

주요 기능

Retrieval of structural variants, gene fusions, and copy number alterations
Automated downloading of somatic mutation datasets and Cancer Gene Census
Support for both current (GRCh38) and legacy (GRCh37) reference genomes
Seamless integration with pandas and pysam for immediate genomic analysis
Access to expert-curated mutational signatures including SBS, DBS, and ID
81 GitHub stars

사용 사례

Automating variant annotation pipelines to identify known cancer-driving mutations
Researching drug resistance mechanisms and clinical annotations for precision medicine
Analyzing mutational signatures across datasets to determine tumor etiology

소개

주요 기능

Retrieval of structural variants, gene fusions, and copy number alterations
Automated downloading of somatic mutation datasets and Cancer Gene Census
Support for both current (GRCh38) and legacy (GRCh37) reference genomes
Seamless integration with pandas and pysam for immediate genomic analysis
Access to expert-curated mutational signatures including SBS, DBS, and ID
81 GitHub stars

사용 사례

Automating variant annotation pipelines to identify known cancer-driving mutations
Researching drug resistance mechanisms and clinical annotations for precision medicine
Analyzing mutational signatures across datasets to determine tumor etiology