bioconductor-linkset
Base Classes for Storing Genomic Link Data
Base Classes for Storing Genomic Link Data
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Provides a comprehensive framework for representing, analyzing, and visualizing genomic interactions, particularly focusing on gene-enhancer relationships. The package extends the GenomicRanges infrastructure to handle paired genomic regions with specialized methods for chromatin interaction data from Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell ATAC-seq experiments. Key features include conversion from common interaction formats, annotation of promoters and enhancers, distance-based analyses, interaction strength metrics, statistical modeling using CHiCANE methodology, and tailored visualization tools. The package aims to standardize the representation of genomic interaction data while providing domain-specific functions not available in general genomic interaction packages.
Summary
Base Classes for Storing Genomic Link Data
Last Updated
Mar 2, 2026 at 21:38
License
MIT + file LICENSE
Supported Platforms