Package: igvShiny 1.9.4

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_1.9.4.tar.gz
igvShiny_1.9.4.zip(r-4.7)igvShiny_1.9.4.zip(r-4.6)igvShiny_1.9.4.zip(r-4.5)
igvShiny_1.9.4.tgz(r-4.6-any)igvShiny_1.9.4.tgz(r-4.5-any)
igvShiny_1.9.4.tar.gz(r-4.7-any)igvShiny_1.9.4.tar.gz(r-4.6-any)
igvShiny_1.9.4.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-1.9.3(bioc 3.24)igvShiny-1.8.3(bioc 3.23)

software shinyapps sequencing coverage

7.61 score 38 stars 1 packages 148 scripts 26 exports 69 dependencies

Last updated from:1ad4317c12. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	173
linux-devel-x86_64	OK	270
source / vignettes	OK	265
linux-release-x86_64	OK	283
macos-release-arm64	OK	126
macos-oldrel-arm64	OK	113
windows-devel	OK	165
windows-release	OK	178
windows-oldrel	OK	163
wasm-release	OK	196

Exports:display get_basic_genomes get_cas_genomes get_css_genomes get_tracks_dir getGenomicRegion getUrl GWASTrack igvShiny igvShinyOutput loadBamTrackFromLocalData loadBamTrackFromURL loadBedGraphTrack loadBedGraphTrackFromURL loadBedTrack loadCramTrackFromURL loadGFF3TrackFromLocalData loadGFF3TrackFromURL loadGwasTrack loadSegTrack loadVcfTrack parseAndValidateGenomeSpec removeTracksByName removeUserAddedTracks renderIgvShiny showGenomicRegion

Dependencies:askpass backports base64enc BiocGenerics bslib cachem checkmate cli cluster colorspace commonmark curl digest evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDbData GenomicRanges glue highr htmltools htmlwidgets httpuv httr IRanges jquerylib jsonlite knitr labeling lambda.r later lifecycle magrittr memoise mime openssl otel promises R6 randomcoloR rappdirs RColorBrewer Rcpp rlang rmarkdown Rtsne S4Vectors sass scales Seqinfo shiny sourcetools stringi stringr sys tinytex V8 vctrs viridisLite withr xfun xtable yaml

igvShiny: a wrapper of IGV in the Shiny apps

Rendered fromigvShiny.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sanitize and merge track configuration options	.sanitizeAndMergeOptions
display the already constructed and configured track	display display,GWASTrack-method
get_basic_genomes	get_basic_genomes
get_cas_genomes	get_cas_genomes
get_css_genomes	get_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.js	get_tracks_dir
the url of the gwas table	getUrl getUrl,GWASTrack-method
Constructor for GWASTrack	.GWASTrack GWASTrack GWASTrack-class
Create an igvShiny instance	igvShiny
create the UI for the widget	igvShinyOutput
load GenomicAlignments data as an igv.js alignment track	loadBamTrackFromLocalData
load a bam track which, with index, is served up by http	loadBamTrackFromURL
load a scored genome annotation track provided as a data.frame	loadBedGraphTrack loadGenomeAnnotationTrack
load a bedgraph track from a URL	loadBedGraphTrackFromURL
load a bed track provided as a data.frame	loadBedTrack
load a cram track which, with index, is served up by http	loadCramTrackFromURL
load a GFF3 track defined by local data	loadGFF3TrackFromLocalData
load a GFF3 track which, with index, is served up by http	loadGFF3TrackFromURL
load a GWAS (genome-wide association study) track provided as a data.frame	loadGwasTrack
load a seg track provided as a data.frame	loadSEGTrack loadSegTrack
load a VCF (variant) track provided as a Bioconductor VariantAnnotation object	loadVcfTrack
parseAndValidateGenomeSpec	parseAndValidateGenomeSpec
remove tracks from the browser	removeTracksByName
remove only those tracks explicitly added by your app	removeUserAddedTracks
draw the igv genome browser element	renderIgvShiny
focus igv on a region	getGenomicRegion showGenomicRegion