methylscaper

methylscaper processes and visualizes data jointly profiling methylation and chromatin accessibility from assays including MAPit, NOMe-seq, scNMT-seq, and nanoNOMe, supporting both single-cell and single-molecule data through ordered representational methylation-state matrices.

Key Features:

• Joint data processing: Handles data from methylation and chromatin accessibility profiling methods including MAPit, NOMe-seq, scNMT-seq, and nanoNOMe.
• Dual data type support: Supports both single-cell and single-molecule data within a common interface.
• Ordered matrix generation: Generates ordered representational methylation-state matrices for joint visualization of both data types.
• Seriation-based ordering: Performs refinement and re-weighting to optimally order cells or DNA molecules for pattern discovery.

Scientific Applications:

• Methylation pattern discovery: Identifies methylation patterns through optimal ordering of cells or DNA molecules.
• Nucleosome positioning: Determines nucleosome positioning from jointly profiled methylation and chromatin accessibility data.

Methodology:

The package uses seriation with interactive refinement and re-weighting to optimally order cells or DNA molecules.