Loop Annotation

关于

Automates the annotation of chromatin interaction data such as Hi-C, HiChIP, and ChIA-PET by identifying regulatory and structural loop types like enhancer-enhancer, enhancer-promoter, and CTCF-CTCF interactions. This skill streamlines the entire bioinformatic workflow, from automatically building enhancer and promoter reference sets when missing to standardizing input formats and generating comprehensive enrichment reports and visualizations. It is an essential tool for researchers seeking to characterize the regulatory landscape or map enhancer-promoter connectivity within specific genomic contexts.

主要功能

• Statistical enrichment analysis of genomic features within interaction sets
• Automated construction of enhancer and promoter reference sets from ATAC and H3K27ac data
• Classification of regulatory (E-P) and structural (CTCF) loop types
• 2 GitHub stars
• Generation of loop type and length distribution visualizations
• Standardization of BEDPE interaction data for downstream tool compatibility

使用场景

• Integrating epigenetic datasets like ATAC-seq and H3K27ac with chromatin loop data
• Analyzing structural chromatin architecture via CTCF orientation and occupancy
• Mapping enhancer-promoter interactions to study gene regulation