methylscaper

methylscaper visualizes joint DNA methylation and chromatin accessibility at single-molecule and single-cell resolution to reveal patterns of nucleosome positioning and transcription factor occupancy.

Key Features:

• Simultaneous Analysis: Visualizes DNA methylation patterns alongside chromatin accessibility, including nucleosome positioning and transcription factor occupancy.
• Weighted Principal Component Analysis (PCA): Orders sequencing reads representing individual epialleles using a weighted PCA algorithm to reveal patterns in nucleosome positioning and transcription factor binding.
• Scalability: Handles large epigenomic datasets efficiently.
• Biological Relevance: Identifies chromatin features that correlate with transcriptional status to aid interpretation of regulatory relationships in disease contexts such as cancer.

Scientific Applications:

• Epigenetic profiling: Simultaneous high-resolution profiling of DNA methylation and chromatin accessibility at single-molecule and single-cell scales.
• Disease and cancer research: Characterization of epigenetic heterogeneity and chromatin-state changes associated with disease development and cancer.
• Biomarker and regulatory element discovery: Identification of potential biomarkers and regulatory elements by linking methylation and accessibility patterns to transcriptional status.

Methodology:

Processes long-read sequencing data from MAPit and scNMT-seq and applies a weighted PCA algorithm to order reads and uncover patterns in epigenetic modifications.