Package: igvShiny 1.9.3

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]

igvShiny_1.9.3.tar.gz
igvShiny_1.9.3.zip(r-4.7)igvShiny_1.9.3.zip(r-4.6)igvShiny_1.9.3.zip(r-4.5)
igvShiny_1.9.3.tgz(r-4.6-any)igvShiny_1.9.3.tgz(r-4.5-any)
igvShiny_1.9.3.tar.gz(r-4.7-any)igvShiny_1.9.3.tar.gz(r-4.6-any)
igvShiny_1.9.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
igvShiny/json (API)
NEWS

# 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-1.9.3(bioc 3.24)igvShiny-1.8.3(bioc 3.23)

softwareshinyappssequencingcoverage

7.42 score 38 stars 1 packages 166 scripts 350 downloads 26 exports 69 dependencies

Last updated from:c955a3e69a. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE181
linux-devel-x86_64OK290
source / vignettesOK259
linux-release-x86_64OK285
macos-release-arm64OK158
macos-oldrel-arm64OK165
windows-develOK173
windows-releaseOK169
windows-oldrelOK181
wasm-releaseOK161

Exports:displayget_basic_genomesget_cas_genomesget_css_genomesget_tracks_dirgetGenomicRegiongetUrlGWASTrackigvShinyigvShinyOutputloadBamTrackFromLocalDataloadBamTrackFromURLloadBedGraphTrackloadBedGraphTrackFromURLloadBedTrackloadCramTrackFromURLloadGFF3TrackFromLocalDataloadGFF3TrackFromURLloadGwasTrackloadSegTrackloadVcfTrackparseAndValidateGenomeSpecremoveTracksByNameremoveUserAddedTracksrenderIgvShinyshowGenomicRegion

Dependencies:askpassbackportsbase64encBiocGenericsbslibcachemcheckmatecliclustercolorspacecommonmarkcurldigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteknitrlabelinglambda.rlaterlifecyclemagrittrmemoisemimeopensslotelpromisesR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsneS4VectorssassscalesSeqinfoshinysourcetoolsstringistringrsystinytexV8vctrsviridisLitewithrxfunxtableyaml

igvShiny: a wrapper of IGV in the Shiny apps

Arkadiusz Gladki

Rendered fromigvShiny.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2024-04-23
Started: 2023-09-18

Readme and manuals

Help Manual

Help pageTopics
Sanitize and merge track configuration options.sanitizeAndMergeOptions
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 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 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 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
focus igv on a regiongetGenomicRegion showGenomicRegion