FreeHiC Spike-In

Overview: FreeHiC Spike-In is an extension of the FreeHi-C (Fragment interactions empirical estimation for fast simulation of Hi-C data) pipeline, specifically designed for simulating and benchmarking differential chromatin interactions. It enables the addition of both data-driven and user-specified spike-ins, allowing researchers to evaluate differential interaction detection methods with known ground truth.

Key Features:

1. Flexible Spike-in Generation:

   • Data-driven spike-in generation
   • User-defined spike-in specification
   • Customizable fold-change thresholds
   • Adjustable spike-in percentages

2. Comprehensive Simulation Pipeline:

   • Fragment-pair interaction processing
   • Bin-pair interaction frequency calculation
   • Integration with FreeHi-C training module
   • Contact matrix simulation

3. Advanced Analysis Options:

   • Neighbor smoothing capabilities
   • Multiple condition comparison
   • Batch processing support
   • Customizable resolution settings

4. User-Friendly Implementation:

   • Clear parameter specifications
   • Extensive documentation
   • Example datasets
   • Step-by-step tutorials

Applications: FreeHiC Spike-In has been successfully applied to:

• Benchmark differential interaction detection methods
• Evaluate method performance with known ground truth
• Simulate realistic Hi-C data with controlled differences
• Study chromatin interaction patterns across conditions

The package is implemented in Python with comprehensive documentation and tutorials to support researchers in the fields of genomics and chromatin biology.

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