Package: GenomicInteractionNodes 1.11.1
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:
GenomicInteractionNodes_1.11.1.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')) |
Bug tracker:https://github.com/jianhong/genomicinteractionnodes/issues
On BioConductor:GenomicInteractionNodes-1.11.0(bioc 3.21)GenomicInteractionNodes-1.10.0(bioc 3.20)
Last updated 30 days agofrom:502619b69d. Checks:5 OK, 2 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 04 2025 |
| R-4.5-win | ERROR | Jan 04 2025 |
| R-4.5-linux | ERROR | Jan 04 2025 |
| R-4.4-win | OK | Jan 04 2025 |
| R-4.4-mac | OK | Jan 04 2025 |
| R-4.3-win | OK | Jan 04 2025 |
| R-4.3-mac | OK | Jan 04 2025 |
Exports:annotateNodescreateRandomNodesdetectNodesenrichmentAnalysis
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate node regions | annotateNodes |
| Create a list of random nodes | createRandomNodes |
| Detect the interaction node | detectNodes |
| Gene ontology enrichment analysis | enrichmentAnalysis |