GenomicInteractionNodes
This package is for version 3.18 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: 3.18
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("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 | ||
| 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 | |
| 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_1.6.0.tar.gz |
| Windows Binary | GenomicInteractionNodes_1.6.0.zip |
| 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 |