Package: annoLinker 1.1.0

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_1.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
annoLinker/json (API)

# Install 'annoLinker' in R:

install.packages('annoLinker', repos = c('https://bioc.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)

network annotation visualization

4.48 score 14 exports 161 dependencies

Last updated from:3cef05638b. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	286
linux-devel-x86_64	OK	538
source / vignettes	OK	403
linux-release-x86_64	OK	533
macos-release-arm64	OK	270
macos-oldrel-arm64	OK	255
windows-devel	OK	437
windows-release	OK	459
windows-oldrel	OK	493
wasm-release	OK	265

Exports:anno_clusters anno_event anno_evidence anno_feature anno_featurebin anno_graph anno_peakbin anno_peaks annoLinker as.data.frame coerce head plotEvidence show

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue gridExtra grImport gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl parallelly pillar pkgconfig png prettyunits progress progressr ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex trackViewer txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridisLite visNetwork withr xfun XML xml2 XVector yaml

annoLinker Vignette: Annotating genomic regions through chromatin interaction links

Introduction | Installation | Quick start | SessionInfo

Rendered fromannoLinker.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotating genomic regions through chromatin interaction links	annoLinker-package
Annotate Peaks with DNA Interaction Networks Using Graph Clustering	annoLinker
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 visualization	plotEvidence