Introduction | Installation | Quick start | Session Info
Package: GenomicInteractionNodes 1.17.0
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:
GenomicInteractionNodes_1.17.0.tar.gz
GenomicInteractionNodes_1.17.0.zip(r-4.7)GenomicInteractionNodes_1.17.0.zip(r-4.6)GenomicInteractionNodes_1.17.0.zip(r-4.5)
GenomicInteractionNodes_1.17.0.tgz(r-4.6-any)GenomicInteractionNodes_1.17.0.tgz(r-4.5-any)
GenomicInteractionNodes_1.17.0.tar.gz(r-4.7-any)GenomicInteractionNodes_1.17.0.tar.gz(r-4.6-any)
GenomicInteractionNodes_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicInteractionNodes/json (API)
| # 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-1.17.0(bioc 3.24)GenomicInteractionNodes-1.16.0(bioc 3.23)
Last updated from:26c86197c8. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 317 | ||
| linux-devel-x86_64 | OK | 610 | ||
| source / vignettes | OK | 401 | ||
| linux-release-x86_64 | OK | 611 | ||
| macos-release-arm64 | OK | 297 | ||
| macos-oldrel-arm64 | OK | 401 | ||
| windows-devel | OK | 412 | ||
| windows-release | OK | 421 | ||
| windows-oldrel | OK | 412 | ||
| wasm-release | OK | 224 |
Exports:annotateNodescreateRandomNodesdetectNodesenrichmentAnalysis
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesglueGO.dbgraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RBGLRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLXVectoryaml
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 |