MutationalPatterns

MutationalPatterns provides an R/Bioconductor package that characterizes and visualizes mutational patterns in base substitution data to analyze mutational signatures, sequence context, transcriptional and replicative strand bias, and genomic distribution.

Key Features:

• Characterization of mutational patterns: Identifies and characterizes mutation types and sequence context, including transcriptional and replicative strand bias and genomic distribution.
• Integration with genomic features: Enables exploration of relationships between mutational patterns and genomic and epigenomic features.
• Quantification of mutational signatures: Quantifies the contribution of known mutational signatures within datasets.
• Visualization: Produces visual representations of mutational spectra, signature contributions, and bias distributions.

Scientific Applications:

• DNA repair mechanisms: Uses mutational patterns to assess disruption or alteration of DNA repair processes and implications for genomic stability.
• Characterization of mutational signatures: Supports detailed characterization and interpretation of known mutational signatures and their activity in samples.

Methodology:

Evaluates mutation types and sequence contexts, assesses transcriptional and replicative strand bias, analyzes genomic distribution patterns, and quantifies contributions of known mutational signatures.