MutSeqR

MutSeqR provides standardized methods for analysis of mutation data following error-corrected sequencing (ECS) for the purpose of mutagenicity assessment.

Key Features:

• Variant Import: Functions import mutation lists provided by a variant caller.
• Statistical Testing: Analytical tools perform statistical testing of mutation data.
• Visualization: Functions support visualization of mutation data.
• Signature Comparison: Mutation data can be compared to COSMIC and/or germline signatures.
• Variant Filtering: Practical variant filtering is available for ECS mutation data.
• Comparative Analysis: The package enables comparative analysis of mutation frequency between experimental conditions.
• Dose-Response Assessment: Benchmark dose calculations support dose-response assessment.
• Mutation Spectrum Analysis: The package performs mutation spectrum analysis.
• Clonality Analysis: Clonality analyses are included in the package functionality.

Scientific Applications:

• Mutagenicity Assessment: The package analyzes ECS mutation data for genetic toxicology studies and mutagenicity testing.
• Genetic Toxicology: MutSeqR supports assessment of mutagenicity and other genetic toxicology endpoints.
• Regulatory Applications: The package facilitates regulatory applications in mutagenicity testing.
• Cross-Platform Reproducibility: Flexible functions enable reproducible analyses across ECS platforms including Duplex Sequencing and SMM-seq.

Methodology:

MutSeqR imports mutation lists provided by a variant caller and applies analytical tools for statistical testing, visualization, signature comparison, variant filtering, comparative analysis of mutation frequency, benchmark dose calculations, mutation spectrum analysis, and clonality analysis.