scool

scool provides a Cooler-derived file format for storing and organizing single-cell Hi-C contact matrices to enable efficient storage, retrieval, and analysis of 3D genome interactions at single-cell resolution.

Key Features:

• Storage efficiency: Reduces the storage burden of single-cell Hi-C datasets and minimizes preprocessing requirements.
• Sparse matrix support: Adapts to sparse interaction matrices while preserving high-resolution data integrity.
• Cooler compatibility: Derives from the established cooler format to maintain compatibility with tools and pipelines that use cooler.
• Stable API support: Provides stable API compatibility from cooler version 0.8.9 onward.

Scientific Applications:

• Single-cell 3D genome analysis: Enables analysis of chromatin interactions and 3D genome organization at single-cell resolution.
• Cell-type-specific regulatory studies: Facilitates investigation of cell-to-cell heterogeneity and cell-type-specific regulatory mechanisms in gene expression.

Methodology:

Adapts the established cooler format for single-cell Hi-C by leveraging cooler's data model, handling sparse interaction matrices, and maintaining high-resolution data integrity.