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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 — BAM and CRAM alignment tracks over BRCA1 (chr17) shown as stacked panels in the embedded IGV browser, alongside the bslib control sidebar
igvShiny demo — BAM and CRAM alignment tracks over BRCA1 (chr17) 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.

More examples live in inst/demos/.

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.