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cosmic-database

Fetch COSMIC mutation data and Cancer Gene Census from authenticated endpoints.

15|2|Updated Dec 17, 2025
Search Tags:#authentication#bioinformatics#mutations#cosmic#vcf#data-download#cancer
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill cosmic-database-rubensliv
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/cosmic-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill cosmic-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Researchers need reliable, programmatic access to COSMIC data (mutations, Cancer Gene Census, signatures, and related resources) to power reproducible cancer genomics analyses, pipeline automation, and cross-study comparisons. This Skill provides authenticated data retrieval and ready-to-use data formats to integrate COSMIC resources into bioinformatics workflows.

Core Features & Use Cases

  • Programmatic COSMIC access: Retrieve core mutations, Cancer Gene Census, mutational signatures, structural variants, copy number, gene expression, and resistance data for analysis pipelines.
  • Pipeline integration: Seamlessly incorporate COSMIC downloads into Python-based or CLI workflows with standard file formats (TSV/CSV/VCF, gzip-compressed).
  • Use Case: A researcher automates nightly downloads of TP53 mutations and Cancer Gene Census genes to maintain an up-to-date mutation atlas for downstream annotation and plotting.

Quick Start

Run the provided download_cosmic.py script with your COSMIC credentials to fetch the latest data files.

Frequently Asked Questions about cosmic-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download COSMIC mutation data programmatically for cancer genomics workflows?▼

Download COSMIC mutation data programmatically by running the provided Python script with valid COSMIC credentials. The skill fetches core mutations, Cancer Gene Census, and mutational signatures as gzip-compressed TSV, CSV, or VCF files ready for bioinformatics pipelines.

Can I integrate COSMIC data downloads into an automated Python pipeline?▼

Yes, you can integrate COSMIC data downloads into automated Python pipelines. The skill uses the requests library to fetch authenticated data, supporting nightly automated downloads of mutations and gene census files for downstream annotation.

Do I need COSMIC credentials to fetch Cancer Gene Census and mutational signature files?▼

Yes, valid COSMIC credentials are required to authenticate and fetch Cancer Gene Census, mutational signatures, and resistance data. The script handles authenticated endpoints to securely retrieve gzip-compressed files for your analysis.

Does this COSMIC data retrieval skill support both GRCh38 and GRCh37 assemblies?▼

Yes, this COSMIC data retrieval skill supports both GRCh38 and GRCh37 genome assemblies. It fetches mutation data, structural variants, and copy number alterations formatted for cross-study comparisons across these reference genomes.

What file formats are available when retrieving COSMIC mutations and structural variants?▼

Available file formats for retrieving COSMIC mutations and structural variants include TSV, CSV, and VCF. All data files are gzip-compressed, ensuring efficient storage and direct compatibility with common Python data-science workflows.

What specific COSMIC resources can I retrieve for gene-level cancer analyses?▼

You can retrieve core mutations, Cancer Gene Census, mutational signatures, structural variants, copy number, gene expression, and resistance data. These resources support data integration and gene-level analyses for comprehensive cancer genomics studies.

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