hictkR

hictk provides high-performance interoperability and processing of Hi-C interaction matrices stored in .hic and Cooler (.cool/.mcool) formats to enable analysis of chromosomal interactions across multiple resolutions.

Key Features:

• Format Interoperability: Operates directly on .hic and Cooler (.cool and .mcool) binary interaction matrix formats to enable access to Hi-C contact data without intermediate format loss.
• Performance Optimization: Implemented in C++ with optimizations for efficient processing of Hi-C datasets at multiple resolutions and with reported benchmarking against other tools.
• Multi-language Bindings: Exposes a C++ library with Python and R bindings for programmatic integration into analysis workflows.
• Conversion Utilities: Provides utilities to convert between .hic and .mcool formats and to perform common interaction-matrix manipulations.
• Multi-resolution Processing: Supports processing of interaction matrices across spatial resolutions, including multi-resolution Cooler (.mcool) representations.

Scientific Applications:

• Genome Organization Analysis: Enables analysis of chromosomal contact maps to study genome organization and spatial genomic architecture using Hi-C data.
• Chromatin Interaction Mapping: Supports identification and characterization of chromatin interactions from Hi-C interaction matrices across resolutions.
• High-Resolution Interaction Mapping: Facilitates processing of high-resolution Hi-C datasets to generate detailed interaction maps from multi-resolution matrices.

Methodology:

Implemented in C++ with a C++ library and Python and R bindings; supports reading and writing .hic and Cooler (.cool/.mcool) binary matrix formats and includes utilities to convert between .hic and .mcool and to process interaction matrices at multiple resolutions.