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GenomicInteractionNodes

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


Bioconductor version: Release (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")

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 1.6.0
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
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Depends On Me
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Package Archives

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

Source Package GenomicInteractionNodes_1.6.0.tar.gz
Windows Binary GenomicInteractionNodes_1.6.0.zip (64-bit only)
macOS Binary (x86_64) GenomicInteractionNodes_1.6.0.tgz
macOS Binary (arm64) GenomicInteractionNodes_1.6.0.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