Package: GenomicInteractionNodes 1.11.3
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_1.11.3.tar.gz
GenomicInteractionNodes_1.11.3.zip(r-4.5)GenomicInteractionNodes_1.11.3.zip(r-4.4)GenomicInteractionNodes_1.11.3.zip(r-4.3)
GenomicInteractionNodes_1.11.3.tgz(r-4.5-any)GenomicInteractionNodes_1.11.3.tgz(r-4.4-any)GenomicInteractionNodes_1.11.3.tgz(r-4.3-any)
GenomicInteractionNodes_1.11.3.tar.gz(r-4.5-noble)GenomicInteractionNodes_1.11.3.tar.gz(r-4.4-noble)
GenomicInteractionNodes_1.11.3.tgz(r-4.4-emscripten)GenomicInteractionNodes_1.11.3.tgz(r-4.3-emscripten)
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-1.11.2(bioc 3.21)GenomicInteractionNodes-1.10.0(bioc 3.20)
Last updated 25 days agofrom:628aad6bd1. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 13 2025 |
| R-4.5-win | OK | Feb 13 2025 |
| R-4.5-mac | OK | Feb 13 2025 |
| R-4.5-linux | OK | Feb 13 2025 |
| R-4.4-win | OK | Feb 13 2025 |
| R-4.4-mac | OK | Feb 13 2025 |
| R-4.3-win | OK | Feb 13 2025 |
| R-4.3-mac | OK | Feb 13 2025 |
Exports:annotateNodescreateRandomNodesdetectNodesenrichmentAnalysis
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml
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 |