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GenomicInteractionNodes

This is the development version of GenomicInteractionNodes; for the stable release version, see GenomicInteractionNodes.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("GenomicInteractionNodes")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews HiC, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License file LICENSE
Depends R (>= 4.2.0), stats
Imports AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors
Linking To
Suggests RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
System Requirements
Enhances
URL https://github.com/jianhong/GenomicInteractionNodes
Bug Reports https://github.com/jianhong/GenomicInteractionNodes/issues
See More
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_1.5.0.tar.gz
Windows Binary GenomicInteractionNodes_1.5.0.zip (64-bit only)
macOS Binary (x86_64) GenomicInteractionNodes_1.5.0.tgz
macOS Binary (arm64) GenomicInteractionNodes_1.5.0.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