linkSet

Base Classes for Storing Genomic Link Data

Bioconductor version: 3.23 · Package version: 1.2.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("linkSet")