CpelTdm.jl

CpelTdm.jl performs differential analysis of DNA methylation by modeling correlated CpG methylation and methylation stochasticity to identify genomic regions with significant methylation differences between sample groups.

Key Features:

• Advanced Statistical Analysis: Incorporates correlations in methylation patterns rather than assuming independent CpG sites to improve specificity and sensitivity of differential detection.
• Methylation Stochasticity Detection: Analyzes methylation entropy and the full probability distribution of methylation states in addition to mean methylation differences.
• Compatibility with Bisulfite Sequencing Technologies: Accepts data from Reduced Representation Bisulfite Sequencing (RRBS), Enriched RRBS (ERRBS), and Whole Genome Bisulfite Sequencing (WGBS).
• User-Specified Target Regions: Performs analyses within genomic regions defined by the user for targeted investigation.
• Implementation: Implemented in Julia.

Scientific Applications:

• Disease epigenetics: Detects genomic regions with differential methylation associated with disease states.
• Developmental epigenetics: Identifies methylation changes linked to developmental processes and cellular differentiation.
• Environmental epigenetics: Detects methylation variability associated with environmental exposures or conditions.

Methodology:

Models correlated CpG methylation within user-defined genomic regions, estimates methylation state probability distributions and entropy, and performs statistical tests for differential methylation between sample groups.