Agent skill · research science · aiskillstore
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Why this skill is useful
Provides specific Python scripts and commands for downloading and processing COSMIC cancer mutation data that the AI wouldn't reliably generate on its own.
What it needs
Requires pandas, requests installed locally. Requires cosmic account access. About 5k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
COSMIC Database Overview COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically. When to Use This Skill This skill should be used when: Downloading cancer mutation data from COSMIC Accessing the Cancer Gene Census for curated cancer gene lists Retrieving mutational signature profiles Querying structural variants, copy number alterations, or gene fusions Analyzing drug resistance mutations Working with cancer cell line genomics data Integrating cancer mutation data into bioinformatics pipelines Researching specific genes or mutations in cancer contexts Prerequisites Account Registration COSMIC requires authentication for data downloads: Academic users: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register Commercial users: License required (contact QIAGEN) Python Requirements Quick Start 1. Basic File Download Use the scripts/downloadcosmic.py script to download COSMIC data files: 2. Command-Line Usage 3. Working with Downloaded Data Available Data Types Core Mutations Download comprehensive mutation data including point mutations, indels, and genomic annotations. Common data types: mutations - Complete coding mutations (TSV format) mutationsvcf - Coding mutations in VCF format sampleinfo - Sample metadata and tumor information Cancer Gene Census Access the expert-curated list of ~700+ cancer genes with substantial evidence of cancer involvement. Use cases: Identifying known cancer genes Filtering variants by cancer relevance Understanding gene roles (oncogene vs tumor suppressor) Target gene selection for research Mutational Signatures Download signature profiles for mutational signature analysis. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/cosmic-database