hicstuff

hicstuff generates and processes Hi-C contact maps to analyze three-dimensional chromosome organization.

Key Features:

• Data representation: Represents genomic proximity data as matrices or contact maps to identify compartments and loops and to correlate these features with transcription and protein occupancy.
• Contact map generation: Generates and handles Hi-C contact maps derived from proximity ligation experiments.
• File format support: Supports formats compatible with cooler (2D bedgraph) and instaGRAAL.
• Normalization and filtering: Implements filtering of events recovered from proximity ligation experiments and applies a balancing normalization procedure to contact maps.
• Visualization: Provides computational visualization of normalized contact data, including the Scalogram utility.
• Organism scope: Applicable to genomes ranging from bacterial nucleoids to larger eukaryotic genomes.

Scientific Applications:

• 3D genome architecture analysis: Analyzes chromosome three-dimensional organization and structural dynamics.
• Proximity ligation assay processing: Processes data from Hi-C, TCC, MicroC (XL), and Hi-CO experiments.
• Chromatin feature detection: Detects compartments and loops and enables correlation of these features with transcription and protein occupancy.
• Cross-organism genomic studies: Supports comparative analyses across bacteria and eukaryotic genomes.

Methodology:

Computational steps explicitly include generation and handling of Hi-C contact maps, filtering of proximity ligation events, application of balancing normalization to contact matrices, visualization of normalized contact data (including Scalogram), and export/import in cooler (2D bedgraph) and instaGRAAL formats.