cosmic-database

Name: cosmic-database
Availability: InStock
Author: OwnLab

Download COSMIC cancer mutation data files via authenticated Python requests.

21|1|Updated Mar 19, 2026

Search Tags:#authentication #python #bioinformatics #mutations #cosmic #data-download #cancer

Ready to run

npx skills add https://github.com/OwnLabAI/ownlab --skill cosmic-database-ownlabai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: cosmic-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/cosmic-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill cosmic-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Access COSMIC cancer mutation data programmatically to support cancer genomics research and reproducible analyses. This includes authenticated downloads of core mutation data, the Cancer Gene Census, mutational signatures, and related data resources.

Core Features & Use Cases

Retrieve core mutation data (e.g., CosmicMutantExport.tsv.gz) for GRCh38 or GRCh37 to feed downstream analyses.
Access Cancer Gene Census, mutational signatures, structural variants, copy number, gene expression, resistance mutations, and sample information for integrated workflows.
Use in data pipelines to filter by gene, merge with expression data, and perform downstream analyses with pandas, R, or bioinformatics tools.

Quick Start

Download the latest COSMIC mutation data for GRCh38 using the provided script and inspect the Cancer Gene Census entries for a gene.

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 for a bioinformatics pipeline?▼

You can download COSMIC cancer mutation data programmatically by running the provided Python script, which uses the requests library to authenticate with your COSMIC account and stream core mutation files like CosmicMutantExport.tsv.gz directly into your pipeline.

Do I need a COSMIC account to access Cancer Gene Census and mutational signatures data?▼

Yes, accessing Cancer Gene Census and mutational signatures data requires a COSMIC account for authentication. The Python script uses your credentials to authenticate the session before fetching and streaming any cancer genomics resources.

Can I retrieve GRCh38 and GRCh37 core mutation data using Python and requests?▼

You can retrieve both GRCh38 and GRCh37 core mutation data using Python and requests. The script authenticates your COSMIC account and fetches the specific genome build's mutation export files for downstream cancer genomics analysis.

What COSMIC data resources are available for cancer genomics research besides core mutations?▼

Besides core mutations, available COSMIC data resources include the Cancer Gene Census, mutational signatures, structural variants, copy number, gene expression, resistance mutations, and sample information for integrated cancer genomics workflows.

What's the best way to integrate COSMIC mutation data with gene expression datasets in pandas or R?▼

The best way to integrate COSMIC data with gene expression datasets is to programmatically download the core mutation files using the Python script, then load the TSV outputs into pandas or R to filter by gene and merge with expression data.

Why does my COSMIC data download script fail during authentication?▼

COSMIC data download scripts fail during authentication if your COSMIC account credentials are invalid or missing. The script requires successful authentication via the requests library before it can stream any cancer mutation or gene census files.