cosmic-database

Download COSMIC cancer genomics datasets using email and password authentication.

557|98|Updated Nov 7, 2025

Search Tags:#bioinformatics #cancer genomics #data download #cosmic #mutation data #gene census

Ready to run

npx skills add https://github.com/jimmc414/Kosmos --skill cosmic-database-jimmc414

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/cosmic-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill cosmic-database-jimmc414

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Catalogue of Somatic Mutations in Cancer (COSMIC), enabling researchers to download and analyze extensive cancer genomics data.

Core Features & Use Cases

Data Download: Download various COSMIC datasets including mutation data, cancer gene census, mutational signatures, and more.
Data Integration: Facilitates the integration of COSMIC data into bioinformatics pipelines and research projects.
Use Case: A researcher needs to identify all known cancer genes with oncogenic roles from the COSMIC Cancer Gene Census to prioritize targets for a new drug discovery project.

Quick Start

Use the cosmic-database skill to download the Cancer Gene Census file using your email and password.

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 cancer mutation data programmatically?▼

To download COSMIC cancer mutation data programmatically, you need a Skill that authenticates using your email and password, then queries datasets like somatic mutations, gene fusions, and copy number alterations across GRCh37 or GRCh38 genome assemblies.

What data types are available in the COSMIC database for cancer genomics research?▼

The COSMIC database provides somatic mutations, the Cancer Gene Census, mutational signatures, gene fusions, and copy number alterations, enabling comprehensive cancer genomics data integration into bioinformatics pipelines.

Do I need a COSMIC account to retrieve Cancer Gene Census and mutation data?▼

Yes, retrieving Cancer Gene Census and mutation data requires user authentication via a registered email and password to access and download COSMIC datasets programmatically.

Can I query COSMIC copy number alterations and gene fusions using pandas and pysam?▼

Querying COSMIC copy number alterations and gene fissions relies on Python dependencies including requests for data retrieval, pandas for data manipulation, and pysam for genomic data processing.

Does the COSMIC database support both GRCh37 and GRCh38 genome assemblies?▼

Yes, the COSMIC database supports querying somatic mutations and other cancer genomics data across both GRCh37 and GRCh38 genome assemblies for flexible genomic coordinate mapping.

How can I identify known oncogenic cancer genes from the COSMIC database for drug discovery?▼

You can identify known oncogenic cancer genes by downloading the COSMIC Cancer Gene Census dataset, which lists genes with documented oncogenic roles to help prioritize targets for drug discovery projects.