How do I use the output in a larger bioinformatics pipeline?

The toolkit outputs structured JSON, which can be piped into 'jq' to extract specific fields or filter genes, making it easy to integrate with tools like bcftools or custom Python scripts.

What is the difference between Tier 1 and Tier 2 genes in the output?

Tier 1 genes have documented activity in cancer with strong evidence of mutations, while Tier 2 genes have strong evidence but less frequent documentation in the literature.

Does this skill include the COSMIC dataset automatically?

No. Due to licensing restrictions, you must register on the COSMIC website and download the 'cancer_gene_census.csv' file manually to the data directory before use.

Is this tool suitable for clinical diagnostics?

This is a research-focused tool designed for data analysis and discovery. All results should be validated by clinical professionals for any medical applications.

Can I process multiple genes at once?

Yes, you can provide multiple space-separated gene symbols or point the toolkit to a text file containing a list of genes for batch processing.

COSMIC Cancer Gene Toolkit

Name: COSMIC Cancer Gene Toolkit
Author: dakesan

bydakesan

Ciencia de Datos y ML

Queries and annotates genomic data using the COSMIC Cancer Gene Census to identify known cancer genes and their clinical properties.

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The COSMIC Toolkit enables bioinformaticians and researchers to programmatically validate gene lists against the expert-curated Catalogue Of Somatic Mutations In Cancer (COSMIC). By integrating directly with the Cancer Gene Census, this skill allows users to retrieve critical metadata including gene tiers, somatic and germline roles, and specific tumor types. It is designed to streamline oncology workflows, such as filtering variant calling results (VCFs) or performing functional gene enrichment, by providing structured JSON output that integrates easily with downstream command-line tools.

Características Principales

Batch processing support for large gene lists via text files
Detailed annotation of gene roles (oncogenes, TSGs, fusions)
0 GitHub stars
Dynamic JSON output compatible with jq for pipeline integration
Programmatic querying of the COSMIC Cancer Gene Census
Identification of Tier 1 and Tier 2 high-confidence cancer genes

Casos de Uso

Classifying research gene sets by their inheritance patterns and mutation types
Annotating VCF candidate genes to prioritize variants in known cancer drivers
Filtering large-scale genomic datasets to focus exclusively on high-confidence Tier 1 genes

Acerca de

Características Principales

Batch processing support for large gene lists via text files
Detailed annotation of gene roles (oncogenes, TSGs, fusions)
0 GitHub stars
Dynamic JSON output compatible with jq for pipeline integration
Programmatic querying of the COSMIC Cancer Gene Census
Identification of Tier 1 and Tier 2 high-confidence cancer genes

Casos de Uso

Classifying research gene sets by their inheritance patterns and mutation types
Annotating VCF candidate genes to prioritize variants in known cancer drivers
Filtering large-scale genomic datasets to focus exclusively on high-confidence Tier 1 genes