Package: igvShiny 1.3.0

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_1.3.0.tar.gz
igvShiny_1.3.0.zip(r-4.5)igvShiny_1.3.0.zip(r-4.4)igvShiny_1.3.0.zip(r-4.3)
igvShiny_1.3.0.tgz(r-4.4-any)igvShiny_1.3.0.tgz(r-4.3-any)
igvShiny_1.3.0.tar.gz(r-4.5-noble)igvShiny_1.3.0.tar.gz(r-4.4-noble)
igvShiny_1.3.0.tgz(r-4.4-emscripten)igvShiny_1.3.0.tgz(r-4.3-emscripten)
igvShiny.pdf |igvShiny.html✨
igvShiny/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://gladkia.github.io

On BioConductor:igvShiny-1.3.0(bioc 3.21)igvShiny-1.2.0(bioc 3.20)

softwareshinyappssequencingcoverage

7.60 score 37 stars 119 scripts 122 downloads 26 exports 73 dependencies

Last updated 2 months agofrom:9a89fc113a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-winNOTEDec 09 2024
R-4.5-linuxNOTEDec 09 2024
R-4.4-winNOTEDec 09 2024
R-4.4-macNOTEDec 09 2024
R-4.3-winNOTEDec 09 2024
R-4.3-macNOTEDec 09 2024

Exports:displayget_basic_genomesget_cas_genomesget_css_genomesget_tracks_dirgetGenomicRegiongetUrlGWASTrackigvShinyigvShinyOutputloadBamTrackFromLocalDataloadBamTrackFromURLloadBedGraphTrackloadBedGraphTrackFromURLloadBedTrackloadCramTrackFromURLloadGFF3TrackFromLocalDataloadGFF3TrackFromURLloadGwasTrackloadSegTrackloadVcfTrackparseAndValidateGenomeSpecremoveTracksByNameremoveUserAddedTracksrenderIgvShinyshowGenomicRegion

Dependencies:askpassbackportsbase64encBiocGenericsbslibcachemcheckmatecliclustercolorspacecommonmarkcrayoncurldigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteknitrlabelinglambda.rlaterlifecyclemagrittrmemoisemimemunsellopensslpromisesR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsneS4VectorssassscalesshinysourcetoolsstringistringrsystinytexUCSC.utilsV8vctrsviridisLitewithrxfunxtableXVectoryamlzlibbioc

igvShiny: a wrapper of IGV in the Shiny apps

Arkadiusz Gladki

Rendered fromigvShiny.Rmdusingknitr::rmarkdownon Dec 09 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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