Single-Nucleus Hi-C Module (chr3d.hic)

Processes single-nucleus Hi-C data from multiple cells. Each cell is processed independently through the standard Hi-C steps, followed by QC filtering, pseudobulk aggregation, and optional clustering.

Overview

The single-nucleus Hi-C module provides a complete pipeline for processing individual cell Hi-C data, including per-cell processing, quality control, pseudobulk aggregation, and optional clustering.

Components

Pipeline Orchestrator

• SnHiCPipeline - Complete sn-Hi-C pipeline orchestrator

Quality Control

• SnHiCCellQC - Cell-level quality control filtering

Pseudobulk

• SnHiCPseudoBulk - Aggregate per-cell matrices into pseudobulk

Documentation

• SnHiC Output Directory Structure - Output directory layout