cosmic-database

What problem does it solve?

Manually navigating and downloading vast cancer mutation data from COSMIC is complex and time-consuming. This Skill automates authenticated access to COSMIC, streamlining cancer research, precision oncology, and bioinformatics pipelines by providing rapid access to critical genomic data.

Core Features & Use Cases

• Mutation Data Download: Retrieve comprehensive somatic mutations (SNVs, indels), structural variants, and gene fusions in TSV, CSV, or VCF formats.
• Cancer Gene Census: Access the expert-curated list of ~700+ cancer genes, including their roles (oncogene, tumor suppressor) and associated mutation types.
• Mutational Signatures: Download signature profiles (SBS, DBS, ID) for advanced mutational signature analysis, aiding in understanding cancer etiology.
• Use Case: Automatically download the latest COSMIC mutation data for a specific gene (e.g., TP53) and filter it by lung cancer samples, providing immediate, actionable insights for targeted therapy research.

Quick Start

Download the Cancer Gene Census (replace with your COSMIC credentials)

from scripts.download_cosmic import download_cosmic_file download_cosmic_file( email="your_email@institution.edu", password="your_password", filepath="GRCh38/cosmic/latest/cancer_gene_census.csv", output_filename="cancer_gene_census.csv" )

Read the downloaded data with pandas

import pandas as pd gene_census = pd.read_csv('cancer_gene_census.csv') print(gene_census.head())