linkSet
This is the development version of linkSet; for the stable release version, see linkSet.
Base Classes for Storing Genomic Link Data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("linkSet")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Coverage, DataRepresentation, HiC, Sequencing, SingleCell, Software |
| Version | 1.3.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |