Files in paul-shannon/igvShiny
igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/GWASTrack.R
R/constants.R
R/genomeSpec.R
R/igvShiny.R
R/packages.R
R/test_igvShiny_package.R
R/utils.R
R/zzz.R
_pkgdown.yml
explore/christianRodhe/myVersion.R
explore/christianRodhe/rstudio-export.zip
explore/christianRodhe/server.R
explore/christianRodhe/ui.R
explore/customReferenceGenome/sars.html
explore/groupAutoscale/groupAutoscale.html
igv.js.examples/1kg-vcf-cram.html
igv.js.examples/arcs-bedpe.html
igv.js.examples/bedGraphUrl.html
igv.js.examples/igv.css
igv.js.examples/spliceJunctionTrack.html
igv.js.examples/tabs-bam.html
inst/demos/customGenomes/customGenome-localFiles-sars.R
inst/demos/customGenomes/customGenome-remoteFiles-sars.R
inst/demos/groupAutoScale.R
inst/demos/igv-cyj-shinyInterference.R
inst/demos/igvShinyDemo-GFF3.R
inst/demos/igvShinyDemo-GWAS.R
inst/demos/igvShinyDemo-GWASTrackClass.R
inst/demos/igvShinyDemo-customGenome-http.R
inst/demos/igvShinyDemo-customGenome-localFiles.R
inst/demos/igvShinyDemo-twoInstances.R
inst/demos/igvShinyDemo-withModules.R
inst/demos/igvShinyDemo-withVCF.R
inst/demos/igvShinyDemo.R
inst/demos/rsconnect.zip
inst/demos/stockGenomesDemo.R
inst/demos/tiny.R
inst/demos/tinyMixCyjIgv.R
inst/extdata/A24_02_01_01.fa
inst/extdata/A24_02_01_01.fa.fai
inst/extdata/A_2_A24_02_01_01.nanopore.minimap.sorted.bam
inst/extdata/GRCh38.94.NDUFS2.gff3
inst/extdata/chr19-cebpaRegion.vcf.gz
inst/extdata/chr19-cebpaRegion.vcf.gz.tbi
inst/extdata/gwas-5k.tsv.gz
inst/extdata/gwas.RData
inst/extdata/ribosomal-RNA-gene.fasta
inst/extdata/ribosomal-RNA-gene.fasta.fai
inst/extdata/ribosomal-RNA-gene.gff3
inst/extdata/sarsGenome/README.txt
inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.101.gff3
inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa
inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai
inst/extdata/sixColumn-demo1.bedpe
inst/extdata/tumor.bam
inst/extdata/tumor.bam.bai
inst/htmlwidgets/igvShiny.js
inst/htmlwidgets/igvShiny.yaml
inst/htmlwidgets/lib/igv-2.12.6.js
inst/htmlwidgets/lib/igv-2.13.1.js
inst/htmlwidgets/lib/igv-268.min.js
inst/htmlwidgets/lib/igv.css
inst/htmlwidgets/lib/igv.js
inst/htmlwidgets/lib/igv.min.js
inst/htmlwidgets/lib/img/cursor_logo.png
inst/htmlwidgets/lib/img/cursor_logo.svg
inst/htmlwidgets/lib/img/igv-logo.svg
inst/unitTests/makefile
inst/unitTests/test_GWASTrack.R
inst/unitTests/test_genomeSpec.R
inst/unitTests/test_shinyApp.R
inst/unitTests/test_utils.R
makefile
man/GWASTrack-class.Rd
man/display.Rd
man/getUrl.Rd
man/get_basic_genomes.Rd
man/get_cas_genomes.Rd
man/get_css_genomes.Rd
man/get_tracks_dir.Rd
man/igvShiny.Rd
man/igvShinyOutput.Rd
man/loadBamTrackFromLocalData.Rd
man/loadBamTrackFromURL.Rd
man/loadBedGraphTrackFromURL.Rd
man/loadBedTrack.Rd
man/loadCramTrackFromURL.Rd
man/loadGFF3TrackFromLocalData.Rd
man/loadGFF3TrackFromURL.Rd
man/loadGenomeAnnotationTrack.Rd
man/loadGwasTrack.Rd
man/loadSEGTrack.Rd
man/loadVcfTrack.Rd
man/parseAndValidateGenomeSpec.Rd
man/removeTracksByName.Rd
man/removeUserAddedTracks.Rd
man/renderIgvShiny.Rd
man/showGenomicRegion.Rd
tests/test_igvShiny_unit_tests.R
vignettes/igvShiny.Rmd
