knowYourCG

KnowYourCG facilitates base-level functional analysis of DNA methylation data by directly targeting CpG dinucleotides with automated supervised screenings of diverse biological and technical influences.

Key Features:

• CpG-level analysis: Directly targets CpG dinucleotides rather than genes or genomic intervals.
• Automated supervised screenings: Screens diverse biological and technical influences including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait-epigenome associations.
• Data sparsity handling: Addresses challenges of data sparsity in low-pass Nanopore sequencing, single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies and epigenetic clocks.
• Efficient infrastructure: Rapidly screens and investigates thousands of knowledgebases.

Scientific Applications:

• Cell differentiation: Provides insights into cell differentiation processes through methylome interpretation.
• Cancer origins: Investigates cancer origins via functional DNA methylation analysis.
• Epigenome-trait associations: Analyzes associations between epigenomes and traits in epigenome-wide association studies.
• Technical issue detection: Identifies array artifacts, single-cell batch effects, and Nanopore 5hmC detection accuracy.

Methodology:

KnowYourCG implements a supervised learning framework with efficient infrastructure for rapid screening and investigation of thousands of knowledgebases.