BandNorm

Overview: BandNorm is a simple yet powerful R package designed for normalizing single-cell Hi-C data. It effectively addresses the challenges of genomic distance bias and sequencing depth variations in single-cell chromatin conformation data through an innovative band normalization approach.

Key Features:

1. Fast Band Normalization:

   • Removes genomic distance bias within cells
   • Normalizes sequencing depth between cells
   • Maintains common band-dependent contact decay profiles
   • Efficient processing of sparse matrices

2. Comprehensive Data Processing:

   • Supports multiple input formats (.hic compatible)
   • Handles batch effect correction
   • Processes sparse matrix representations
   • Integrates with existing Hi-C analysis pipelines

3. Visualization and Analysis Tools:

   • PCA-based dimension reduction
   • UMAP and t-SNE visualizations
   • Cell clustering analysis
   • Quality control metrics

4. User-Friendly Interface:

   • Simple function calls for complex operations
   • Extensive documentation and tutorials
   • Example datasets
   • Integration with other R packages

Applications: BandNorm has been successfully applied to various single-cell Hi-C datasets, enabling researchers to:

• Normalize chromatin interaction frequencies
• Remove technical biases in scHi-C data
• Compare cells across different experimental conditions
• Integrate with other single-cell analysis tools

The package is implemented in R with comprehensive documentation and tutorials to support researchers in the fields of genomics and single-cell biology.