Package: orthoRibbon 0.99.0

Jianhong Ou

orthoRibbon: Ribbon-Diagram Visualization of Orthologous Genes Across Species

OrthoRibbon is a visualization toolkit for displaying orthologous gene relationships across species using ribbon-based diagrams. It enables intuitive comparison of conserved genes and genomic correspondence between chromosomes or genomic regions. The package supports flexible input formats and produces publication-quality figures for comparative genomics and evolutionary analysis.

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

orthoRibbon_0.99.0.tar.gz
orthoRibbon_0.99.0.zip(r-4.7-any)orthoRibbon_0.99.0.zip(r-4.6-any)orthoRibbon_0.99.0.zip(r-4.5-any)
orthoRibbon_0.99.0.tgz(r-4.6-any)orthoRibbon_0.99.0.tgz(r-4.5-any)
orthoRibbon_0.99.0.tar.gz(r-4.7-any)orthoRibbon_0.99.0.tar.gz(r-4.6-any)
orthoRibbon_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
orthoRibbon/json (API)

# Install 'orthoRibbon' in R:

install.packages('orthoRibbon', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

visualization annotation comparativegenomics

3.65 score 9 exports 148 dependencies

Last updated from:1dcc5e520e. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	235
linux-devel	OK	468
source / vignettes	OK	365
linux-release	OK	376
macos-release	OK	380
macos-oldrel	OK	351
windows-devel	OK	366
windows-release	OK	371
windows-oldrel	OK	368
wasm-release	OK	214

Exports:buildBezierDF buildPlotData getGeneGRs getGeneIDs getHomologGRs getHomologIDs HomologPlotData orthoRibbonPlot subset

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib ca cachem cigarillo cli cluster codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray digest dir.expiry dplyr evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus geneClusterPattern generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggplot2 ggrepel glue grImport gtable highr hms htmltools htmlwidgets httr httr2 InteractionSet IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl permute pillar pkgconfig png polyclip prettyunits progress purrr pwalign qap R6 RANN rappdirs RColorBrewer Rcpp RCurl registry restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seriation snow SparseArray strawr stringi stringr SummarizedExperiment sys systemfonts tibble tidyr tidyselect tinytex trackViewer TSP tweenr txdbmaker UCSC.utils utf8 vctrs vegan viridisLite withr xfun XML xml2 XVector yaml

orthoRibbon Vignette: Ribbon-Diagram Visualization of Orthologous Genes Across Species

Rendered fromorthoRibbon.Rmdusingknitr::rmarkdown

Last update: 2026-10-02
Started: 2026-03-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Ribbon-based visualization of orthologous genes across species	orthoRibbon-package orthoRibbon
Build the data.frame for B\'ezier curve	buildBezierDF
Build the plot data	buildPlotData
Retrieve all the gene ranges	getGeneGRs
Retrieve all the Ensembl gene IDs by given species abbreviations	getGeneIDs
Retrieve the homolog pairs	getHomologGRs
Retrieve the homolog pairs	getHomologIDs
HomologPlotData S4 class	"names",HomologPlotData-method "[",HomologPlotData,ANY,ANY,ANY-method "[[",HomologPlotData,ANY,ANY-method $,HomologPlotData-method $<-,HomologPlotData-method .DollarNames,HomologPlotData,character-method .DollarNames.HomologPlotData HomologPlotData HomologPlotData-class names,HomologPlotData-method subset,HomologPlotData,list-method subset,HomologPlotData-method [,HomologPlotData,ANY,ANY,ANY-method [[,HomologPlotData,ANY,ANY-method
Plot the data	orthoRibbonPlot