├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GWASTrack.R ├── constants.R ├── genomeSpec.R ├── igvShiny.R ├── packages.R ├── utils.R └── zzz.R ├── _pkgdown.yml ├── explore ├── christianRodhe │ ├── myVersion.R │ ├── rstudio-export.zip │ ├── server.R │ └── ui.R ├── customReferenceGenome │ └── sars.html └── groupAutoscale │ └── groupAutoscale.html ├── igv.js.examples ├── 1kg-vcf-cram.html ├── arcs-bedpe.html ├── bedGraphUrl.html ├── igv.css ├── spliceJunctionTrack.html └── tabs-bam.html ├── inst ├── demos │ ├── customGenomes │ │ ├── customGenome-localFiles-sars.R │ │ └── customGenome-remoteFiles-sars.R │ ├── groupAutoScale.R │ ├── igv-cyj-shinyInterference.R │ ├── igvShinyDemo-GFF3.R │ ├── igvShinyDemo-GWAS.R │ ├── igvShinyDemo-GWASTrackClass.R │ ├── igvShinyDemo-customGenome-http.R │ ├── igvShinyDemo-customGenome-localFiles.R │ ├── igvShinyDemo-twoInstances.R │ ├── igvShinyDemo-withModules.R │ ├── igvShinyDemo-withVCF.R │ ├── igvShinyDemo.R │ ├── rsconnect.zip │ ├── stockGenomesDemo.R │ ├── tiny.R │ └── tinyMixCyjIgv.R ├── extdata │ ├── A24_02_01_01.fa │ ├── A24_02_01_01.fa.fai │ ├── A_2_A24_02_01_01.nanopore.minimap.sorted.bam │ ├── GRCh38.94.NDUFS2.gff3 │ ├── chr19-cebpaRegion.vcf.gz │ ├── chr19-cebpaRegion.vcf.gz.tbi │ ├── gwas-5k.tsv.gz │ ├── gwas.RData │ ├── ribosomal-RNA-gene.fasta │ ├── ribosomal-RNA-gene.fasta.fai │ ├── ribosomal-RNA-gene.gff3 │ ├── sarsGenome │ │ ├── README.txt │ │ ├── Sars_cov_2.ASM985889v3.101.gff3 │ │ ├── Sars_cov_2.ASM985889v3.dna.toplevel.fa │ │ └── Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai │ ├── sixColumn-demo1.bedpe │ ├── tumor.bam │ └── tumor.bam.bai └── htmlwidgets │ ├── igvShiny.js │ ├── igvShiny.yaml │ └── lib │ ├── igv-2.12.6.js │ ├── igv-2.13.1.js │ ├── igv-268.min.js │ ├── igv.css │ ├── igv.js │ ├── igv.min.js │ └── img │ ├── cursor_logo.png │ ├── cursor_logo.svg │ └── igv-logo.svg ├── makefile ├── man ├── GWASTrack-class.Rd ├── display.Rd ├── dot-sanitizeAndMergeOptions.Rd ├── getUrl.Rd ├── get_basic_genomes.Rd ├── get_cas_genomes.Rd ├── get_css_genomes.Rd ├── get_tracks_dir.Rd ├── igvShiny.Rd ├── igvShinyOutput.Rd ├── loadBamTrackFromLocalData.Rd ├── loadBamTrackFromURL.Rd ├── loadBedGraphTrackFromURL.Rd ├── loadBedTrack.Rd ├── loadCramTrackFromURL.Rd ├── loadGFF3TrackFromLocalData.Rd ├── loadGFF3TrackFromURL.Rd ├── loadGenomeAnnotationTrack.Rd ├── loadGwasTrack.Rd ├── loadSEGTrack.Rd ├── loadVcfTrack.Rd ├── parseAndValidateGenomeSpec.Rd ├── removeTracksByName.Rd ├── removeUserAddedTracks.Rd ├── renderIgvShiny.Rd └── showGenomicRegion.Rd ├── tests ├── testthat.R └── testthat │ ├── test-GWAStrack.R │ ├── test-genomeSpec.R │ ├── test-shinyApp.R │ └── test-utils.R └── vignettes └── igvShiny.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/check-bioc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/.github/workflows/check-bioc.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2023 2 | COPYRIGHT HOLDER: igvShiny authors 3 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/GWASTrack.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/GWASTrack.R -------------------------------------------------------------------------------- /R/constants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/constants.R -------------------------------------------------------------------------------- /R/genomeSpec.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/genomeSpec.R -------------------------------------------------------------------------------- /R/igvShiny.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/igvShiny.R -------------------------------------------------------------------------------- /R/packages.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/packages.R -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/utils.R -------------------------------------------------------------------------------- /R/zzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/R/zzz.R -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /explore/christianRodhe/myVersion.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/christianRodhe/myVersion.R -------------------------------------------------------------------------------- /explore/christianRodhe/rstudio-export.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/christianRodhe/rstudio-export.zip -------------------------------------------------------------------------------- /explore/christianRodhe/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/christianRodhe/server.R -------------------------------------------------------------------------------- /explore/christianRodhe/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/christianRodhe/ui.R -------------------------------------------------------------------------------- /explore/customReferenceGenome/sars.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/customReferenceGenome/sars.html -------------------------------------------------------------------------------- /explore/groupAutoscale/groupAutoscale.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/explore/groupAutoscale/groupAutoscale.html -------------------------------------------------------------------------------- /igv.js.examples/1kg-vcf-cram.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/1kg-vcf-cram.html -------------------------------------------------------------------------------- /igv.js.examples/arcs-bedpe.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/arcs-bedpe.html -------------------------------------------------------------------------------- /igv.js.examples/bedGraphUrl.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/bedGraphUrl.html -------------------------------------------------------------------------------- /igv.js.examples/igv.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/igv.css -------------------------------------------------------------------------------- /igv.js.examples/spliceJunctionTrack.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/spliceJunctionTrack.html -------------------------------------------------------------------------------- /igv.js.examples/tabs-bam.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/igv.js.examples/tabs-bam.html -------------------------------------------------------------------------------- /inst/demos/customGenomes/customGenome-localFiles-sars.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/customGenomes/customGenome-localFiles-sars.R -------------------------------------------------------------------------------- /inst/demos/customGenomes/customGenome-remoteFiles-sars.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/customGenomes/customGenome-remoteFiles-sars.R -------------------------------------------------------------------------------- /inst/demos/groupAutoScale.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/groupAutoScale.R -------------------------------------------------------------------------------- /inst/demos/igv-cyj-shinyInterference.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igv-cyj-shinyInterference.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-GFF3.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-GFF3.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-GWAS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-GWAS.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-GWASTrackClass.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-GWASTrackClass.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-customGenome-http.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-customGenome-http.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-customGenome-localFiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-customGenome-localFiles.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-twoInstances.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-twoInstances.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-withModules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-withModules.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo-withVCF.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo-withVCF.R -------------------------------------------------------------------------------- /inst/demos/igvShinyDemo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/igvShinyDemo.R -------------------------------------------------------------------------------- /inst/demos/rsconnect.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/rsconnect.zip -------------------------------------------------------------------------------- /inst/demos/stockGenomesDemo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/stockGenomesDemo.R -------------------------------------------------------------------------------- /inst/demos/tiny.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/tiny.R -------------------------------------------------------------------------------- /inst/demos/tinyMixCyjIgv.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/demos/tinyMixCyjIgv.R -------------------------------------------------------------------------------- /inst/extdata/A24_02_01_01.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/A24_02_01_01.fa -------------------------------------------------------------------------------- /inst/extdata/A24_02_01_01.fa.fai: -------------------------------------------------------------------------------- 1 | A24_02_01_01 3502 14 80 81 2 | -------------------------------------------------------------------------------- /inst/extdata/A_2_A24_02_01_01.nanopore.minimap.sorted.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/A_2_A24_02_01_01.nanopore.minimap.sorted.bam -------------------------------------------------------------------------------- /inst/extdata/GRCh38.94.NDUFS2.gff3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/GRCh38.94.NDUFS2.gff3 -------------------------------------------------------------------------------- /inst/extdata/chr19-cebpaRegion.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/chr19-cebpaRegion.vcf.gz -------------------------------------------------------------------------------- /inst/extdata/chr19-cebpaRegion.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/chr19-cebpaRegion.vcf.gz.tbi -------------------------------------------------------------------------------- /inst/extdata/gwas-5k.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/gwas-5k.tsv.gz -------------------------------------------------------------------------------- /inst/extdata/gwas.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/gwas.RData -------------------------------------------------------------------------------- /inst/extdata/ribosomal-RNA-gene.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/ribosomal-RNA-gene.fasta -------------------------------------------------------------------------------- /inst/extdata/ribosomal-RNA-gene.fasta.fai: -------------------------------------------------------------------------------- 1 | U13369.1 42999 54 70 71 2 | -------------------------------------------------------------------------------- /inst/extdata/ribosomal-RNA-gene.gff3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/ribosomal-RNA-gene.gff3 -------------------------------------------------------------------------------- /inst/extdata/sarsGenome/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/sarsGenome/README.txt -------------------------------------------------------------------------------- /inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.101.gff3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.101.gff3 -------------------------------------------------------------------------------- /inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa -------------------------------------------------------------------------------- /inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai: -------------------------------------------------------------------------------- 1 | MN908947.3 29903 87 60 61 2 | -------------------------------------------------------------------------------- /inst/extdata/sixColumn-demo1.bedpe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/sixColumn-demo1.bedpe -------------------------------------------------------------------------------- /inst/extdata/tumor.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/tumor.bam -------------------------------------------------------------------------------- /inst/extdata/tumor.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/extdata/tumor.bam.bai -------------------------------------------------------------------------------- /inst/htmlwidgets/igvShiny.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/igvShiny.js -------------------------------------------------------------------------------- /inst/htmlwidgets/igvShiny.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/igvShiny.yaml -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv-2.12.6.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv-2.12.6.js -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv-2.13.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv-2.13.1.js -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv-268.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv-268.min.js -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv.css -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv.js -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/igv.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/igv.min.js -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/img/cursor_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/img/cursor_logo.png -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/img/cursor_logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/img/cursor_logo.svg -------------------------------------------------------------------------------- /inst/htmlwidgets/lib/img/igv-logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/inst/htmlwidgets/lib/img/igv-logo.svg -------------------------------------------------------------------------------- /makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/makefile -------------------------------------------------------------------------------- /man/GWASTrack-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/GWASTrack-class.Rd -------------------------------------------------------------------------------- /man/display.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/display.Rd -------------------------------------------------------------------------------- /man/dot-sanitizeAndMergeOptions.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/dot-sanitizeAndMergeOptions.Rd -------------------------------------------------------------------------------- /man/getUrl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/getUrl.Rd -------------------------------------------------------------------------------- /man/get_basic_genomes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/get_basic_genomes.Rd -------------------------------------------------------------------------------- /man/get_cas_genomes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/get_cas_genomes.Rd -------------------------------------------------------------------------------- /man/get_css_genomes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/get_css_genomes.Rd -------------------------------------------------------------------------------- /man/get_tracks_dir.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/get_tracks_dir.Rd -------------------------------------------------------------------------------- /man/igvShiny.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/igvShiny.Rd -------------------------------------------------------------------------------- /man/igvShinyOutput.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/igvShinyOutput.Rd -------------------------------------------------------------------------------- /man/loadBamTrackFromLocalData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadBamTrackFromLocalData.Rd -------------------------------------------------------------------------------- /man/loadBamTrackFromURL.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadBamTrackFromURL.Rd -------------------------------------------------------------------------------- /man/loadBedGraphTrackFromURL.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadBedGraphTrackFromURL.Rd -------------------------------------------------------------------------------- /man/loadBedTrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadBedTrack.Rd -------------------------------------------------------------------------------- /man/loadCramTrackFromURL.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadCramTrackFromURL.Rd -------------------------------------------------------------------------------- /man/loadGFF3TrackFromLocalData.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadGFF3TrackFromLocalData.Rd -------------------------------------------------------------------------------- /man/loadGFF3TrackFromURL.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadGFF3TrackFromURL.Rd -------------------------------------------------------------------------------- /man/loadGenomeAnnotationTrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadGenomeAnnotationTrack.Rd -------------------------------------------------------------------------------- /man/loadGwasTrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadGwasTrack.Rd -------------------------------------------------------------------------------- /man/loadSEGTrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadSEGTrack.Rd -------------------------------------------------------------------------------- /man/loadVcfTrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/loadVcfTrack.Rd -------------------------------------------------------------------------------- /man/parseAndValidateGenomeSpec.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/parseAndValidateGenomeSpec.Rd -------------------------------------------------------------------------------- /man/removeTracksByName.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/removeTracksByName.Rd -------------------------------------------------------------------------------- /man/removeUserAddedTracks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/removeUserAddedTracks.Rd -------------------------------------------------------------------------------- /man/renderIgvShiny.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/renderIgvShiny.Rd -------------------------------------------------------------------------------- /man/showGenomicRegion.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/man/showGenomicRegion.Rd -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-GWAStrack.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/tests/testthat/test-GWAStrack.R -------------------------------------------------------------------------------- /tests/testthat/test-genomeSpec.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/tests/testthat/test-genomeSpec.R -------------------------------------------------------------------------------- /tests/testthat/test-shinyApp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/tests/testthat/test-shinyApp.R -------------------------------------------------------------------------------- /tests/testthat/test-utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/tests/testthat/test-utils.R -------------------------------------------------------------------------------- /vignettes/igvShiny.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gladkia/igvShiny/HEAD/vignettes/igvShiny.Rmd --------------------------------------------------------------------------------