mutSignatures

mutSignatures extracts and analyzes DNA mutational signatures from somatic mutation catalogs to characterize patterns of DNA damage and repair in cancer.

Key Features:

• R implementation (v2.1): Provided as an R package implementing the computational methods described.
• Integrated computational framework: Tailored for analysis of mutational signatures in cancer genomes.
• Import DNA variants: Functions to import DNA variant data and somatic mutation catalogs.
• Compute mutation types: Algorithms to compute mutation types from variant data.
• Signature extraction (NMF): Extracts mutational signatures using non-negative matrix factorization (NMF).
• Correlation analysis: Enables association of extracted signatures with clinical and molecular features.

Scientific Applications:

• Deciphering mutational signatures: Identifies distinct non-random mutational patterns from somatic mutation data.
• Correlation with clinical and molecular features: Associates mutational signatures with clinical and molecular characteristics across cancer types.
• Analysis of smoking-related cancers: Applied to smoking-related cancer datasets to characterize signatures consistent with independent studies.
• Discovery of complementary patterns: Reveals complementary or previously unrecognized mutational patterns in cancer genomes.

Methodology:

Imports DNA variant data, computes mutation types, and applies non-negative matrix factorization (NMF) to extract mutational signatures from somatic mutation catalogs.