Peak-Based Analysis Module (chr3d.peak_based)
Contains modules for peak-based chromatin interaction analysis, shared between ChIA-PET and HiChIP pipelines.
Overview
The peak-based module provides components for ChIA-PET and HiChIP analysis, including PET mapping, pipeline orchestration, and fragment-based purification.
Components
Mapping
- PETMapperV3 - Maps ChIA-PET tags to reference genome
Pipeline Orchestrators
- ChiaPetPipeline - End-to-end ChIA-PET pipeline
- HiChIPPipeline - End-to-end HiChIP pipeline
Purification
- FragmentIndex - In-memory fragment index for overlap lookup
- purify_bedpe - Purify BEDPE by removing same-fragment PETs
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