linkSet
This is thereleased version of linkSet; for the devel version, seelinkSet.
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: 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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("linkSet")| Hi-C Workflow with linkSet | HTML | R Script |
| linkSet: Base Classes for Storing Genomic Link Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage,DataRepresentation,HiC,Sequencing,SingleCell,Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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/linkSethttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | linkSet_1.0.0.tar.gz |
| Windows Binary (x86_64) | linkSet_1.0.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/linkSet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/linkSet |
| Bioc Package Browser | https://code.bioconductor.org/browse/linkSet/ |
| Package Short Url | https://bioconductor.org/packages/linkSet/ |
| Package Downloads Report | Download Stats |