MethylC-analyzer

MethylC-analyzer performs comprehensive downstream analysis of genome-wide DNA methylation data from bisulfite sequencing (WGBS, RRBS) and enzymatic methyl-seq (EM-seq) to quantify and interpret CG and non-CG (CHG, CHH) methylation patterns across genomic contexts.

Key Features:

• Versatile Methylation Analysis: Analyzes post-alignment bisulfite sequencing data from WGBS, RRBS, and EM-seq and quantifies methylation in CG and non-CG contexts (CHG, CHH).
• Genome-Wide Visualization: Processes aligned sequencing data together with gene location files to generate genome-wide methylation profiles and meta-plots for specific genomic elements.
• Differential Methylation Analysis: Identifies differentially methylated regions (DMRs) and assesses enrichment of associated genomic features.
• Cross-Genomic Applicability: Validated on plant and human bisulfite sequencing data, enabling analysis across diverse species and genomic contexts.

Scientific Applications:

• Epigenetic profiling: Characterizes DNA methylation landscapes to study epigenetic modifications.
• Plant and fungal methylation studies: Enables analysis of non-CG methylation patterns (CHG, CHH) prevalent in plant and fungal genomes.
• Gene regulation and development: Supports investigations into gene expression regulation and developmental processes via region-specific methylation analysis and DMR detection.
• Disease epigenetics: Facilitates studies of disease etiology linked to epigenetic changes through identification of DMRs and methylation-pattern visualization.

Methodology:

Processes post-alignment bisulfite sequencing data and gene location files to compute methylation levels in CG, CHG, and CHH contexts, generate genome-wide profiles and meta-plots, and detect DMRs and genomic-feature enrichment; implemented in Python and R.