Package: igvShiny 1.9.51

Arkadiusz Gladki

igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.

Authors:Paul Shannon [aut], Arkadiusz Gladki [aut, cre], Karolina Scigocka [aut], Carolina Heimann [ctb], Steffen Klasberg [ctb], Vincent Carey [ctb], Parv Sachdeva [ctb], Mateusz Gladki [ctb], R Consortium [fnd]

igvShiny_1.9.51.tar.gz
igvShiny_1.9.51.zip(r-4.7-any)igvShiny_1.9.51.zip(r-4.6-any)igvShiny_1.9.51.zip(r-4.5-any)
igvShiny_1.9.51.tgz(r-4.6-any)igvShiny_1.9.51.tgz(r-4.5-any)
igvShiny_1.9.51.tar.gz(r-4.7-any)igvShiny_1.9.51.tar.gz(r-4.6-any)
igvShiny_1.9.51.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
igvShiny/json (API)

# Install 'igvShiny' in R:
install.packages('igvShiny', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gladkia/igvshiny/issues

Pkgdown/docs site:https://gladkia.github.io

On BioConductor:igvShiny-1.9.49(bioc 3.24)igvShiny-1.8.3(bioc 3.23)

softwareshinyappssequencingcoverage

9.36 score 46 stars 1 packages 188 scripts 412 downloads 34 exports 71 dependencies

Last updated from:bd7a6a83fd. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE250
linux-develOK370
source / vignettesOK285
linux-releaseOK262
macos-releaseOK184
macos-oldrelOK156
windows-develOK213
windows-releaseOK179
windows-oldrelOK197
wasm-releaseOK197

Exports:checkReferenceCompatibilitydisplayget_basic_genomesget_cas_genomesget_css_genomesget_tracks_dirgetGenomicRegiongetUrlGWASTrackigvShinyigvShinyOutputloadBamTrackFromLocalDataloadBamTrackFromLocalFileloadBamTrackFromURLloadBedGraphTrackloadBedGraphTrackFromURLloadBedTrackloadCramTrackFromLocalDataloadCramTrackFromLocalFileloadCramTrackFromURLloadGFF3TrackFromLocalDataloadGFF3TrackFromURLloadGwasTrackloadSegTrackloadSpliceJunctionTrackFromLocalDataloadSpliceJunctionTrackFromURLloadVcfTrackparseAndValidateGenomeSpecremoveTracksByNameremoveUserAddedTracksrenderIgvShinyserveLocalFileshowshowGenomicRegion

Dependencies:askpassbackportsbase64encBiocGenericsbslibcachemcheckmatecliclustercolorspacecommonmarkcurldigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteknitrlabelinglambda.rlaterlifecyclemagrittrmemoisemimeopensslotelpromisesR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsneS4VectorssassscalesSeqinfoshinysourcetoolsstringistringrsystinytexUCSC.utilsV8vctrsviridisLitewithrxfunxtableyaml

Track options reference
What this vignette is | How an option reaches the browser | Loaders | Options every track accepts | Numeric tracks: bedGraph, wig, bigWig | Annotation tracks: bed, gff3 | Alignment tracks: bam, cram | Variant tracks: vcf | GWAS tracks | Splice junction tracks | Options on startup tracks | When an option seems to do nothing | Session Info
Rendered fromtrack-options.Rmdusingknitr::rmarkdown

Last update: 2026-09-11
Started: 2026-07-31

Getting started with igvShiny
Who this is for | Install | The three moving parts | A complete app | Loading a track from your own data | Loading tracks at startup | Drawing two tracks in one panel | Moving around, and knowing where you are | Inside a Shiny module | Stock genomes | Custom genomes | When something does not show up | Where to go next | Session Info
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-08-01
Started: 2026-07-25

Readme and manuals

Help Manual

Help pageTopics
Pack junction attributes into a bed name column.packJunctionAttributes
Sanitize and merge track configuration options.sanitizeAndMergeOptions
Check a chromosome color map before it reaches igv.js.sanitizeChromosomeColorMap
Sanitize one startup track specification.sanitizeTrack
Sanitize a list of startup track specifications.sanitizeTracks
Check reference compatibility between track data and genome specificationcheckReferenceCompatibility
display the already constructed and configured trackdisplay display,GWASTrack-method
get_basic_genomesget_basic_genomes
get_cas_genomesget_cas_genomes
get_css_genomesget_css_genomes
get_tracks_dir Get the directory where tracks are stored. The directory can be defined with environmental variable. If not defined the default is a directory called "tracks" in the temp directory. We need a local directory to write files - for instance, a vcf file representing a genomic region of interest. We then tell shiny about that directory, so that shiny's built-in http server can serve up files we write there, ultimately consumed by igv.jsget_tracks_dir
the url of the gwas tablegetUrl getUrl,GWASTrack-method
Constructor for GWASTrack.GWASTrack GWASTrack GWASTrack-class
Create an igvShiny instanceigvShiny
create the UI for the widgetigvShinyOutput
load GenomicAlignments data as an igv.js alignment trackloadBamTrackFromLocalData
Load a BAM Track from a Local File via HTTP Range RequestsloadBamTrackFromLocalFile
load a bam track which, with index, is served up by httploadBamTrackFromURL
load a scored genome annotation track provided as a data.frameloadBedGraphTrack loadGenomeAnnotationTrack
load a bedgraph track from a URLloadBedGraphTrackFromURL
load a bed track provided as a data.frameloadBedTrack
load a cram file sitting on the same machine as the shiny apploadCramTrackFromLocalData loadCramTrackFromLocalFile
load a cram track which, with index, is served up by httploadCramTrackFromURL
load a GFF3 track defined by local dataloadGFF3TrackFromLocalData
load a GFF3 track which, with index, is served up by httploadGFF3TrackFromURL
load a GWAS (genome-wide association study) track provided as a data.frameloadGwasTrack
load a seg track provided as a data.frameloadSEGTrack loadSegTrack
load a splice junction track from a data.frameloadSpliceJunctionTrackFromLocalData
load a splice junction track served up by httploadSpliceJunctionTrackFromURL
load a VCF (variant) track provided as a Bioconductor VariantAnnotation objectloadVcfTrack
parseAndValidateGenomeSpecparseAndValidateGenomeSpec
remove tracks from the browserremoveTracksByName
remove only those tracks explicitly added by your appremoveUserAddedTracks
draw the igv genome browser elementrenderIgvShiny
Serve a local file via HTTP Range Requests from the Shiny sessionserveLocalFile
Display a short summary of a GWASTrack objectshow,GWASTrack-method
focus igv on a regiongetGenomicRegion showGenomicRegion