cosmic-database

Download COSMIC cancer mutation data programmatically using Python scripts that handle authentication and retrieve datasets like CosmicMutantExport.tsv.gz. The Skill provides functions to specify genome assembly (GRCh38/GRCh37), dataset type, and file format (TSV, CSV, VCF), then load results directly into pandas for analysis.

Access core COSMIC datasets including mutations, Cancer Gene Census, mutational signatures, structural variants, fusions, copy number, gene expression, and resistance mutations. All datasets support multiple genome assemblies and file formats for integration into cancer genomics workflows.

Yes, this Skill supports VCF file format alongside TSV and CSV for COSMIC data downloads. You can retrieve mutation data in VCF format and integrate it with pysam for variant annotation and downstream bioinformatics analyses.

The Skill enforces authentication handling for both academic and commercial COSMIC access. Authentication credentials are managed through the Python functions, enabling secure, reproducible data downloads across research and clinical contexts.

Yes, the Skill requires pandas for data manipulation, requests for authenticated downloads, and pysam for VCF file handling. These dependencies enable loading COSMIC datasets into Python workflows for downstream analysis and integration.

Use the Skill's CLI and Python functions to download relevant COSMIC datasets, specify genome assembly and file format, then load data into pandas DataFrames. Combine with variant annotation and signature analysis tools to build reproducible precision oncology workflows.