GenomicInteractionNodes

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractionNodes.

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


Bioconductor version: 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>

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

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

Details

biocViews HiC, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License file LICENSE
Depends R (>= 4.2.0), stats
Imports AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors
System Requirements
URL https://github.com/jianhong/GenomicInteractionNodes
Bug Reports https://github.com/jianhong/GenomicInteractionNodes/issues
See More
Suggests RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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 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
Old Source Packages for BioC 3.16 Source Archive