Package: GenomicInteractionNodes 1.16.0

Jianhong Ou

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

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.

Authors:Jianhong Ou [aut, cre], Yarui Diao [fnd]

GenomicInteractionNodes_1.16.0.tar.gz
GenomicInteractionNodes_1.16.0.zip(r-4.7)GenomicInteractionNodes_1.16.0.zip(r-4.6)GenomicInteractionNodes_1.16.0.zip(r-4.5)
GenomicInteractionNodes_1.16.0.tgz(r-4.6-any)GenomicInteractionNodes_1.16.0.tgz(r-4.5-any)
GenomicInteractionNodes_1.16.0.tar.gz(r-4.7-any)GenomicInteractionNodes_1.16.0.tar.gz(r-4.6-any)
GenomicInteractionNodes_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GenomicInteractionNodes/json (API)
NEWS

# Install 'GenomicInteractionNodes' in R:
install.packages('GenomicInteractionNodes', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jianhong/genomicinteractionnodes/issues

On BioConductor:GenomicInteractionNodes-1.17.0(bioc 3.24)GenomicInteractionNodes-1.16.0(bioc 3.23)

hicsequencingsoftware

4.65 score 6 scripts 294 downloads 4 exports 69 dependencies

Last updated from:de5a2b437e (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE249
linux-devel-x86_64OK582
source / vignettesOK379
linux-release-x86_64OK591
macos-release-arm64OK311
macos-oldrel-arm64OK335
windows-develOK425
windows-releaseOK467
windows-oldrelOK417
wasm-releaseOK211

Exports:annotateNodescreateRandomNodesdetectNodesenrichmentAnalysis

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLXVectoryaml

GenomicInteractionNodes Guide

Jianhong Ou, Yu Xiang, Xiaolin Wei, and Yarui Diao

Rendered fromGenomicInteractionNodes_vignettes.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2022-04-11
Started: 2022-04-11