├── .Rbuildignore ├── .github ├── CODE_OF_CONDUCT.md ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── comprehensive.yml │ ├── pin-app.yml │ ├── quick.yml │ ├── release.yml │ └── rhub.yaml ├── .gitignore ├── CONTRIBUTING.md ├── DESCRIPTION ├── Deployment.md ├── DockerDeploy ├── Dockerfile ├── LICENSE ├── LICENSE.md ├── Makefile ├── NAMESPACE ├── NEWS.md ├── OmicNavigator.Rproj ├── R ├── add.R ├── app.R ├── check.R ├── combine.R ├── data.R ├── dropdowns.R ├── export.R ├── get.R ├── import.R ├── local.R ├── overlaps.R ├── plots.R ├── print.R ├── sanitize.R ├── summary.R ├── tests.R ├── upset.R ├── utility.R ├── validate.R └── zzz.R ├── README.md ├── data └── RNAseq123.RData ├── inst ├── CITATION ├── OmicNavigator.gif ├── extdata │ └── description-fields-reserved.txt └── tinytest │ ├── backwardsCompatibility │ ├── ONstudytest20251015_0.1.0.tar.gz │ └── README.md │ ├── testAdd.R │ ├── testApp.R │ ├── testBackwardsCompatibility.R │ ├── testBugs.R │ ├── testCheck.R │ ├── testCombine.R │ ├── testDropdowns.R │ ├── testExport.R │ ├── testExtraMetadata.R │ ├── testGet.R │ ├── testGetNumeric.R │ ├── testImport.R │ ├── testLibraries.R │ ├── testMetaAssays.R │ ├── testOverlaps.R │ ├── testPiecemeal.R │ ├── testPlot.R │ ├── testPrint.R │ ├── testSummary.R │ ├── testUpset.R │ ├── testUtility.R │ ├── testValidate.R │ └── tinytestSettings.R ├── man ├── Mm.c2.Rd ├── OmicNavigator-package.Rd ├── addAnnotations.Rd ├── addAssays.Rd ├── addBarcodes.Rd ├── addEnrichments.Rd ├── addEnrichmentsLinkouts.Rd ├── addFeatures.Rd ├── addMapping.Rd ├── addMetaAssays.Rd ├── addMetaFeatures.Rd ├── addMetaFeaturesLinkouts.Rd ├── addModels.Rd ├── addObjects.Rd ├── addOverlaps.Rd ├── addPlots.Rd ├── addReports.Rd ├── addResults.Rd ├── addResultsLinkouts.Rd ├── addSamples.Rd ├── addTests.Rd ├── basal.vs.lp.Rd ├── basal.vs.ml.Rd ├── cam.BasalvsLP.Rd ├── cam.BasalvsML.Rd ├── combineStudies.Rd ├── createStudy.Rd ├── exportStudy.Rd ├── figures │ └── omicnavigator-dark-text.png ├── getAnnotations.Rd ├── getAssays.Rd ├── getBarcodeData.Rd ├── getBarcodes.Rd ├── getEnrichments.Rd ├── getEnrichmentsAnnotations.Rd ├── getEnrichmentsIntersection.Rd ├── getEnrichmentsLinkouts.Rd ├── getEnrichmentsModels.Rd ├── getEnrichmentsNetwork.Rd ├── getEnrichmentsStudies.Rd ├── getEnrichmentsTable.Rd ├── getEnrichmentsUpset.Rd ├── getFavicons.Rd ├── getFeatures.Rd ├── getInstalledStudies.Rd ├── getLinkFeatures.Rd ├── getMapping.Rd ├── getMetaAssays.Rd ├── getMetaFeatures.Rd ├── getMetaFeaturesLinkouts.Rd ├── getMetaFeaturesTable.Rd ├── getModels.Rd ├── getNodeFeatures.Rd ├── getObjects.Rd ├── getOverlaps.Rd ├── getPackageVersion.Rd ├── getPlots.Rd ├── getPlottingData.Rd ├── getReportLink.Rd ├── getReports.Rd ├── getResults.Rd ├── getResultsIntersection.Rd ├── getResultsLinkouts.Rd ├── getResultsModels.Rd ├── getResultsStudies.Rd ├── getResultsTable.Rd ├── getResultsTests.Rd ├── getResultsUpset.Rd ├── getSamples.Rd ├── getStudyMeta.Rd ├── getTests.Rd ├── getUpsetCols.Rd ├── group.Rd ├── importStudy.Rd ├── installApp.Rd ├── installStudy.Rd ├── lane.Rd ├── lcpm.Rd ├── plotStudy.Rd ├── removeStudy.Rd ├── samplenames.Rd ├── shared-add.Rd ├── shared-data.Rd ├── shared-dropdowns.Rd ├── shared-get.Rd ├── shared-upset.Rd ├── startApp.Rd ├── summary.onStudy.Rd └── validateStudy.Rd ├── scripts ├── RNAseq123.R ├── bump-app-version.R ├── bundleApp.sh ├── diagrams │ ├── enrichments-1.gv │ ├── enrichments-2.gv │ ├── enrichments-3.gv │ ├── enrichments-rna.gv │ ├── models.gv │ ├── results-1.gv │ ├── results-2.gv │ ├── results-3.gv │ └── results-rna.gv ├── install-dependencies-r2u.sh ├── install-test-study.R └── release.sh ├── tests └── tinytest.R └── vignettes ├── .gitignore ├── OmicNavigatorAPI.Rnw ├── OmicNavigatorUsersGuide.Rnw └── images ├── enrichments-1.pdf ├── enrichments-2.pdf ├── enrichments-3.pdf ├── enrichments-rna.pdf ├── models.pdf ├── results-1.pdf ├── results-2.pdf ├── results-3.pdf └── results-rna.pdf /.Rbuildignore: 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