linkSet
This is the released version of linkSet; for the devel version, see linkSet.
Base Classes for Storing Genomic Link Data
Bioconductor version: Release (3.23)
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] 
Maintainer: Gilbert Han <GilbertHan1011 at gmail.com>
citation("linkSet")):Gilbert Han. linkSet: Base Classes for Storing Genomic Link Data. doi:10.18129/B9.bioc.linkSet, R package version 1.2.0, https://bioconductor.org/packages/linkSet.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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
| No vignettes available | |
| Reference Manual |
Details
| biocViews | Coverage, DataRepresentation, HiC, Sequencing, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | GenomicRanges, S4Vectors, R (>= 4.5.0) |
| Imports | methods, IRanges, GenomeInfoDb, BiocGenerics, Organism.dplyr, InteractionSet, ggplot2, patchwork, scales, foreach, iterators, stats, rlang, MASS, data.table, DBI, doParallel, AnnotationDbi |
| System Requirements | |
| URL | https://github.com/GilbertHan1011/linkSet https://gilberthan1011.github.io/linkSet |
| Bug Reports | https://github.com/GilbertHan1011/linkSet/issues/new |
See More
| Suggests | knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Hs.eg.db, GenomicFeatures, GenomicInteractions, gamlss, gamlss.tr, BiocStyle, rtracklayer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | linkSet_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | linkSet_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | linkSet_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/linkSet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/linkSet |
| Package Short Url | https://bioconductor.org/packages/linkSet/ |
| Package Downloads Report | Download Stats |