NanoMethViz

NanoMethViz visualizes methylation data from Oxford Nanopore long-read sequencing to support analysis of DNA base modifications such as 5-methylcytosine.

Key Features:

• Compatibility with Multiple Callers: Parses methylation calls from nanopolish, f5c, and megalodon.
• Efficient Data Management: Stores methylation data in a compressed format to handle large nanopore datasets.
• Sample-Level Analysis: Performs multidimensional scaling for unsupervised exploration of relationships between sample methylation profiles.
• Feature-Class Aggregation: Aligns genomic feature classes (e.g., genes, CpG islands) to relative positions and aggregates methylation profiles across features.
• High-Resolution Spaghetti Plots: Plots methylation patterns along individual reads for per-read visualization across genomic regions.
• Integration with Bioconductor: Interoperates with Bioconductor objects and workflows.

Scientific Applications:

• Comparative Methylation Analysis: Comparing DNA methylation profiles between experimental groups to identify differential patterns.
• Feature-Centric Methylation Studies: Investigating methylation patterns across genes and CpG islands to study biological processes and disease-associated changes.
• High-Throughput Nanopore Studies: Analyzing large-scale Oxford Nanopore methylation datasets.

Methodology:

Parses nanopolish, f5c, and megalodon outputs into a compressed data format, applies multidimensional scaling for sample-level analysis, aligns features to relative positions for aggregated profiles, and generates per-read spaghetti plots.