GenomicInteractionNodes

DOI: 10.18129/B9.bioc.GenomicInteractionNodes  

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

Bioconductor version: Release (3.16)

The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.

Author: Jianhong Ou [aut, cre], Yarui Diao [fnd]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("GenomicInteractionNodes")

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("GenomicInteractionNodes")

 

HTML	R Script	GenomicInteractionNodes Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	HiC, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	file LICENSE
Depends	R (>= 4.2.0), stats
Imports	AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/jianhong/GenomicInteractionNodes
BugReports	https://github.com/jianhong/GenomicInteractionNodes/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GenomicInteractionNodes_1.2.0.tar.gz
Windows Binary	GenomicInteractionNodes_1.2.0.zip
macOS Binary (x86_64)	GenomicInteractionNodes_1.2.0.tgz
macOS Binary (arm64)	GenomicInteractionNodes_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicInteractionNodes
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicInteractionNodes
Bioc Package Browser	https://code.bioconductor.org/browse/GenomicInteractionNodes/
Package Short Url	https://bioconductor.org/packages/GenomicInteractionNodes/
Package Downloads Report	Download Stats