epialleleR

epialleleR provides a computational framework for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data.

Key Features:

• Epiallele-aware methylation calling: Performs fast methylation calling with awareness of epiallele structure in NGS data.
• Allele-specific methylation analysis: Enables sensitive detection of allele-specific methylation patterns through linkage to epihaplotype data.
• Mosaic epimutation detection: Detects and quantifies low-level mosaic methylation events such as those affecting the BRCA1 gene promoter.
• Visualisation: Provides visualisation capabilities for methylation analysis results.

Scientific Applications:

• Cancer epigenetics research: Detects low-level mosaic methylation of tumour suppressor gene promoters such as BRCA1 associated with elevated cancer risk.
• Translational epigenetics: Supports translational research on mosaic epigenetic events as contributors to cancer burden.
• Methylation sequencing data analysis: Analyses methylation sequencing data from simulated and real data sets for epimutation detection.

Methodology:

Linkage to epihaplotype data is used to detect low-level methylation events; performance was assessed using simulated and real data sets.