FreeHiC

Overview: FreeHi-C (Fragment interactions empirical estimation for fast simulation of Hi-C data) is a powerful data-driven simulator for Hi-C and other 3D proximity ligation sequencing data. Version 2.0 introduces enhanced capabilities including a spike-in module for simulating differential chromatin interactions, making it an invaluable tool for benchmarking and method development in 3D genomics.

Key Features:

1. High-Fidelity Data Simulation:

   • Non-parametric interaction distribution estimation
   • Fragment-level interaction modeling
   • Data-driven simulation approach
   • High biological relevance

2. Comprehensive Processing Pipeline:

   • Raw sequencing data processing
   • Fragment interaction frequency calculation
   • Contact matrix generation
   • Differential interaction simulation

3. Performance Optimization:

   • C/C++ accelerated computing
   • Parallel processing support
   • Memory-efficient implementation
   • Docker container support

4. Flexible Analysis Options:

   • Multiple input format support
   • Customizable simulation parameters
   • Integration with downstream analysis
   • Extensive quality control

Applications: FreeHiC has been successfully applied to:

• Benchmark Hi-C analysis methods
• Power analysis through data augmentation
• False discovery rate control
• Method development and validation
• Differential interaction studies

The package is implemented in Python with C/C++ acceleration for computationally intensive components, providing comprehensive documentation and tutorials to support researchers in the fields of genomics and chromatin biology.

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