Package: GenomicInteractionNodes 1.11.0

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_1.11.0.tar.gz
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GenomicInteractionNodes.pdf |GenomicInteractionNodes.html✨
GenomicInteractionNodes/json (API)
NEWS

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

Peer review:

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

On BioConductor:GenomicInteractionNodes-1.11.0(bioc 3.21)GenomicInteractionNodes-1.10.0(bioc 3.20)

hicsequencingsoftware

4.30 score 1 scripts 125 downloads 4 exports 72 dependencies

Last updated 2 months agofrom:60276ee299. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winERRORNov 29 2024
R-4.5-linuxERRORNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:annotateNodescreateRandomNodesdetectNodesenrichmentAnalysis

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc

GenomicInteractionNodes Guide

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

Rendered fromGenomicInteractionNodes_vignettes.Rmdusingknitr::rmarkdownon Nov 29 2024.

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