- Home
- Bioconductor 3.22
- Software Packages
- linkSet
linkSet
This is the released version of linkSet; for the devel version, see linkSet.
Base Classes for Storing Genomic Link Data
Bioconductor version: Release (3.22)
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.
Author: Gilbert Han [aut, cre] ORCID iD ORCID: 0009-0000-0293-2467
Maintainer: Gilbert Han <GilbertHan1011 at gmail.com>
citation("linkSet")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("linkSet")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("linkSet")
Details
See More
Package Archives
Follow Installation instructions to use this package in your R session.