mutation-analysis-for-gene

What problem does it solve?

Enables researchers to identify and quantify somatic mutations in a specified gene across TCGA cohorts, providing mutation frequencies, hotspot residues, and mutation-type classifications alongside publication-ready visualizations.

Core Features & Use Cases

• Cross-cohort mutation profiling: Aggregate somatic mutations for a gene across TCGA PanCancer Atlas studies.
• Hotspot detection: Identify recurrent amino-acid positions and summarize mutation types at hotspots.
• Multi-format outputs: Generate a mutation_summary.tsv, lollipop_plot.png, mutation_frequency.png, mutation_types.png, and hotspot_details.tsv for downstream analysis.
• Flexible data sources: Query cBioPortal by default and optionally consume a local MAF file as a fallback or supplement.
• Use Case: A researcher analyzes TP53 mutations to compare mutation burden and hotspot distribution between breast cancer and lung cancer cohorts, with ready-to-publish charts.

Quick Start

Run the mutation analysis by specifying a gene and optional mutation file to generate mutation summaries and visualizations.