Package: annoLinker 1.0.0

Jianhong Ou

annoLinker: Annotating genomic regions through chromatin interaction links

Fast annotation of genomic peaks using DNA interaction data by constructing interaction networks with igraph, where peaks overlapping any node in a connected subgraph are annotated with all genes in that subgraph. The annotation evidence could be visualized as either a network graph or a genomic track integrated with gene annotation information.

Authors:Jianhong Ou [aut, cre], Kenneth Poss [aut, fnd]

annoLinker_1.0.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
annoLinker/json (API)
NEWS

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

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

On BioConductor:annoLinker-1.1.0(bioc 3.24)annoLinker-1.0.0(bioc 3.23)

networkannotationvisualization

4.48 score 179 downloads 14 exports 160 dependencies

Last updated from:a5bf22b78b (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE287
linux-devel-x86_64OK542
source / vignettesOK404
linux-release-x86_64OK585
macos-release-arm64OK336
macos-oldrel-arm64OK303
windows-develOK490
windows-releaseOK505
windows-oldrelOK418
wasm-releaseOK228

Exports:anno_clustersanno_eventanno_evidenceanno_featureanno_featurebinanno_graphanno_peakbinanno_peaksannoLinkeras.data.framecoerceheadplotEvidenceshow

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdir.expirydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsgluegridExtragrImportgtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslparallellypillarpkgconfigpngprettyunitsprogressprogressrProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextrackViewertxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitevisNetworkwithrxfunXMLxml2XVectoryaml

annoLinker Vignette: Annotating genomic regions through chromatin interaction links

Jianhong Ou

Rendered fromannoLinker.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2026-01-22
Started: 2025-10-23

Readme and manuals

Help Manual

Help pageTopics
Annotating genomic regions through chromatin interaction linksannoLinker-package
Annotate Peaks with DNA Interaction Networks Using Graph ClusteringannoLinker
Class '"annoLinkerResult"'annoLinkerResult annoLinkerResult-class anno_clusters anno_clusters,annoLinkerResult-method anno_event anno_event,annoLinkerResult,numeric-method anno_event,annoLinkerResult-method anno_evidence anno_evidence,annoLinkerResult,numeric-method anno_evidence,annoLinkerResult-method anno_feature anno_feature,annoLinkerResult,numeric-method anno_feature,annoLinkerResult-method anno_featurebin anno_featurebin,annoLinkerResult,numeric-method anno_featurebin,annoLinkerResult-method anno_graph anno_graph,annoLinkerResult-method anno_peakbin anno_peakbin,annoLinkerResult,numeric-method anno_peakbin,annoLinkerResult-method anno_peaks anno_peaks,annoLinkerResult-method as.data.frame,annoLinkerResult-method coerce coerce,annoLinkerResult,GRanges-method head,annoLinkerResult,ANY-method head,annoLinkerResult-method length,annoLinkerResult-method show,annoLinkerResult-method
Plot interaction network for visualizationplotEvidence