GenomicInteractionNodes
This is the released version of GenomicInteractionNodes; for the devel version, see GenomicInteractionNodes.
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
Bioconductor version: Release (3.23)
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 <jou at morgridge.org>
citation("GenomicInteractionNodes")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | file LICENSE |
| Depends | R (>= 4.2.0), stats |
| Imports | AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, Seqinfo, 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | GenomicInteractionNodes_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicInteractionNodes_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicInteractionNodes_1.16.0.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 |