methplotlib

methplotlib visualizes and analyzes modified nucleotides detected by Oxford Nanopore Technologies sequencing to enable inspection and quantification of DNA methylation patterns.

Key Features:

• Input support: Accepts nanopolish output and methylation frequency files generated by scripts such as calculate_methylation_frequency.py for downstream analysis.
• Visualization of methylation: Displays per-site methylation calls and methylation frequency profiles derived from nanopore sequencing data.
• Statistical analysis: Provides scripts for analysing allele-specific modifications and testing differential modification frequency across subjects.

Scientific Applications:

• DNA methylation profiling: Inspection and quantification of methylation patterns at nucleotide resolution from nanopore data.
• Allele-specific modification analysis: Detection and analysis of allele-specific methylation within subjects.
• Differential methylation studies: Comparison of modification frequencies across subjects for studies of epigenetic variation and disease-associated changes.

Methodology:

Parses nanopolish outputs and methylation frequency files (e.g., calculate_methylation_frequency.py) and applies provided statistical scripts for allele-specific and differential modification frequency analyses.