methrix

methrix provides a toolset for systematic aggregation and analysis of whole-genome bisulfite sequencing (WGBS) data, summarizing bedGraph files into methylation and coverage matrices.

Key Features:

• bedGraph reader: Summarizes methylation calls based on annotated reference indices, infers and collapses strands, handles uncovered reference CpG sites, and facilitates flexible input file format specification.
• Quality control filtering: Optimized functions for filtering WGBS results based on quality metrics.
• Subsetting: Optimized functions for selecting subsets of WGBS data.
• Visualization: Optimized functions for visualizing WGBS results.
• DMR integration: Easy integration with tools for differentially methylated region calling and annotation.

Scientific Applications:

• WGBS data processing: Systematic analysis of large whole-genome bisulfite sequencing datasets through efficient computational processing.
• Genome-wide methylation analysis: Facilitation of genome-wide DNA methylation analysis through integration with differentially methylated region calling and annotation tools.

Methodology:

methrix reads bedGraph or similar tab-separated text files and summarizes methylation calls based on annotated reference indices, with strand inference and collapsing, and handling of uncovered reference CpG sites.