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igvShiny

An htmlwidget wrapper of the Integrative Genomics Viewer (IGV) — embed an interactive genome browser in your Shiny apps, and drive it from R. One of only two Bioconductor packages bridging IGV to R.

🔬 Live demo

gladkia-igvshiny-demo.share.connect.posit.cloud

Click through BED / BedGraph / GWAS / BAM / CRAM tracks in a running app — no install required. (Hosted on Posit Connect Cloud; source in demo/posit-connect/.)

igvShiny demo — hg38 BAM and CRAM alignment tracks over the APP region on chr21 shown as stacked panels in the embedded IGV browser, alongside the bslib control sidebar
igvShiny demo — hg38 BAM and CRAM alignment tracks over the APP region on chr21 shown as stacked panels in the embedded IGV browser, alongside the bslib control sidebar

Installation

Release version from Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("igvShiny")

Development version from GitHub:

remotes::install_github("gladkia/igvShiny")

Quick start 

library(shiny)
library(igvShiny)

options <- parseAndValidateGenomeSpec(genomeName = "hg38", initialLocus = "NDUFS2")

ui <- fluidPage(
  igvShinyOutput("igv")
)

server <- function(input, output, session) {
  output$igv <- renderIgvShiny({
    igvShiny(options)
  })
}

shinyApp(ui, server)

From there, load tracks reactively with the load*Track* functions (loadBedTrack, loadBedGraphTrack, loadGwasTrack, loadBamTrackFromURL, loadCramTrackFromURL, …) and move the view with showGenomicRegion().

Features

  • Interactive IGV genome browser as a Shiny htmlwidget, usable as a Shiny module.
  • Stock genomes (hg38, hg19, mm10, tair10, …) and custom genomes from local or remote FASTA.
  • Track loaders for BED, BedGraph, bed9, GWAS, SEG, VCF, BAM (URL / local), and CRAM (URL).
  • Navigate and query the current view from R (showGenomicRegion(), getGenomicRegion()).
  • Track-click events surfaced back to the Shiny server.

Runnable apps live in inst/demos/, one per topic: igvShinyDemo.R (most of the API — this is what the live demo serves), tiny.R, genomes.R, gwas.R, local-data.R, modules.R, two-instances.R. Run one with shiny::runApp(system.file("demos", "tiny.R", package = "igvShiny")).

Documentation

Contributing

Contributions are welcome — please open an issue or pull request. The package follows Bioconductor coding and review standards (see AGENTS.md).

License

MIT © the igvShiny authors (see LICENSE.md / DESCRIPTION). Originally created by Paul Shannon; lead developer and maintainer: Arkadiusz Gladki.