SwDMR

SwDMR identifies differentially methylated regions (DMRs) from whole genome bisulfite sequencing (WGBS) data to detect methylation differences across samples for epigenetic analysis.

Key Features:

• WGBS input: Accepts whole genome bisulfite sequencing (WGBS) data for genome-wide methylation analysis.
• Sliding window approach: Employs a sliding window method to systematically scan genomic regions for methylation variation.
• No-replicate support: Detects methylation differences between samples even when biological replicates are not available.
• Statistical hypothesis testing: Implements accessible statistical methods tailored for hypothesis testing across two or more samples.
• Multiple test correction: Controls the false discovery rate through multiple test correction procedures.
• Downstream analyses: Provides modules for clustering, annotation, and visualization of identified DMRs.
• Comprehensive DMR output: Produces detailed information on differential methylation to support functional interpretation.

Scientific Applications:

• Gene expression regulation: Used to study DNA methylation changes associated with regulation of gene expression.
• Chromatin dynamics and remodeling: Applied to investigate chromatin remodeling and chromatin dynamics via methylation patterns.
• Epigenetic studies in health and disease: Supports investigations of epigenetic modifications and their roles in health and disease.
• Functional region discovery: Helps uncover potential functional genomic regions involved in epigenetic regulation.

Methodology:

Performs a sliding window genome scan on WGBS data, applies statistical hypothesis testing across two or more samples, uses multiple test correction to control false discovery rate, and includes downstream clustering, annotation, and visualization of DMRs.