Describe the four assemblies | One all-vs-all track between them | Stack them in a synteny view | The same PAF as a dotplot | Building the PAF from your own genomes
Package: JBrowseR 0.11.0
Colin Diesh
JBrowseR: An R Interface to the JBrowse 2 Genome Browser
Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.
Authors:
JBrowseR_0.11.0.tar.gz
JBrowseR_0.11.0.zip(r-4.7-any)JBrowseR_0.11.0.zip(r-4.6-any)JBrowseR_0.11.0.zip(r-4.5-any)
JBrowseR_0.11.0.tgz(r-4.6-any)JBrowseR_0.11.0.tgz(r-4.5-any)
JBrowseR_0.11.0.tar.gz(r-4.7-any)JBrowseR_0.11.0.tar.gz(r-4.6-any)
JBrowseR_0.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
JBrowseR/json (API)
| # Install 'JBrowseR' in R: |
| install.packages('JBrowseR', repos = c('https://gmod.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gmod/jbrowser/issues
Pkgdown/docs site:https://gmod.github.io
genomicsreactjsrmarkdownshinyvisualization
Last updated from:7d3c096e8c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 130 | ||
| source / vignettes | OK | 175 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 95 | ||
| macos-oldrel-arm64 | OK | 79 | ||
| windows-devel-x86_64 | OK | 79 | ||
| windows-release-x86_64 | OK | 119 | ||
| windows-oldrel-x86_64 | OK | 79 | ||
| wasm-release | OK | 117 |
Exports:assemblydotplot_viewJBrowseRJBrowseRAppJBrowseROutputlinear_viewrenderJBrowseRsynteny_tracksynteny_viewtext_indexthemetracktrack_data_frametracksview
Dependencies:base64encbslibcachemclidigestevaluatefastmapfontawesomefshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclememoisemimeR6rappdirsrlangrmarkdownsasstinytexxfunyaml
Comparing genomes: linear synteny and dotplots
Last update: 2026-07-22
Started: 2026-07-18
Introduction to JBrowseR
The one-liner | Adding tracks | A gallery | Where to next
Last update: 2026-07-22
Started: 2021-02-16
Advanced JSON tutorial
When to use it | From a config file | From an R list
Last update: 2026-07-22
Started: 2021-02-18
Custom browser tutorial
Describe the assembly | Add tracks | Enable gene-name search | Put it together | Show results computed in R | Reacting to clicks in Shiny
Last update: 2026-07-22
Started: 2021-02-17
Hosting data for JBrowseR
Server requirements | Viewing local files
Last update: 2026-07-11
Started: 2021-02-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Describe a genome assembly from a FASTA URL | assembly |
| Describe a dotplot view comparing two assemblies | dotplot_view |
| Embed a JBrowse 2 linear genome view | JBrowseR |
| Shiny bindings for JBrowseR | JBrowseR-shiny JBrowseROutput renderJBrowseR |
| Embed the full JBrowse 2 app (multiple views of any type) | JBrowseRApp |
| Describe a linear genome view for 'JBrowseRApp(views = ...)' | linear_view |
| Build a synteny (PAF) track config spanning two assemblies | synteny_track |
| Describe a linear synteny view comparing two (or more) assemblies | synteny_view |
| Describe a gene-name text-search index | text_index |
| Build a custom color theme | theme |
| Describe a data track by its URL | track |
| Build a track from an R data frame | track_data_frame |
| Collect tracks into a list for JBrowseR | tracks |
| Describe a view for 'JBrowseRApp(views = ...)' | view |
