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>

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")

 

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: