musicatk

musicatk enables comprehensive mutational signature analysis by counting and combining multiple mutation types and calculating strand features for signature discovery and exposure inference.

Key Features:

• Multi-mutation type support: Counts and combines SBS, DBS, and indels in mutational signature inference.
• Strand feature calculation: Calculates replication strand, transcription strand, and combinations of these features.
• Genomic feature discovery: Discovers signatures from unique and proprietary genomic features associated with any mutation type.
• Signature discovery methods: Implements several methods for discovery of new mutational signatures.
• Exposure inference: Provides methods to infer exposure given an existing set of signatures.
• Signature comparison and matching: Compares signatures between cohorts and finds matching signatures in COSMIC V2 or COSMIC V3.

Scientific Applications:

• Mutational signature inference: Identifies carcinogenic exposures or aberrant cellular processes that cause alterations to the genome.
• Cross-cohort signature analysis: Compares mutational signatures between different patient cohorts.
• COSMIC signature matching: Matches discovered signatures against known reference signatures in COSMIC V2 or COSMIC V3 databases.

Methodology:

musicatk implements several methods for discovery of new signatures and methods to infer exposure given an existing set of signatures.