scGAD

Overview: scGAD (single-cell Gene Associating Domain) is an innovative R package designed for analyzing single-cell Hi-C data at the gene level. It enables the extraction of three-dimensional chromatin interactions and facilitates the integration of single-cell 3D genomics with other single-cell modalities.

Key Features:

1. Gene-level 3D Chromatin Analysis:

   • Extracts chromatin interactions at gene resolution
   • Provides gene-centric view of 3D genome organization
   • Enables functional interpretation of chromatin structure

2. Single-cell Data Integration:

   • Integrates 3D genomics with other single-cell modalities
   • Supports multi-modal data analysis
   • Facilitates comprehensive understanding of cellular states

3. Advanced Analytical Tools:

   • Robust normalization methods
   • Statistical framework for interaction detection
   • Visualization tools for 3D genome structure
   • Integration with other single-cell analysis pipelines

4. Comprehensive Documentation:

   • Detailed tutorials and vignettes
   • Example datasets and use cases
   • Best practices for analysis workflow

Applications: scGAD has been successfully applied to various single-cell Hi-C datasets, providing insights into chromatin organization at single-cell resolution and its relationship with gene regulation and cellular function.

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

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