msPIPE

msPIPE performs end-to-end analysis of whole-genome bisulfite sequencing (WGBS) data to generate DNA methylation profiles, compute methylation levels in annotated genomic regions, and identify hypomethylated and differentially methylated regions.

Key Features:

• Comprehensive Workflow: Performs end-to-end processing of WGBS data from initial pre-processing to downstream methylation analyses.
• Methylation Profiling: Generates detailed methylation profiles and statistical summaries and calculates methylation levels within functional genomic regions using annotations.
• Advanced Analysis Capabilities: Supports hypomethylation analysis and differential methylation analysis to identify significant methylation changes across conditions or sample types.
• Visualization Tools: Produces publication-quality figures representing methylation profiles and analysis results.

Scientific Applications:

• Gene regulation studies: Enables analysis of DNA methylation patterns relevant to transcriptional regulation.
• Biomarker identification: Supports discovery of methylation-based biomarkers for disease or phenotype association studies.
• Epigenetics in development and environment: Facilitates investigation of methylation changes involved in development and environmental responses.

Methodology:

Connects WGBS pre-processing steps to downstream analyses including methylation profiling, statistical summaries, calculation of methylation levels in annotated regions, hypomethylation analysis, differential methylation analysis, and visualization.