R: Open-Source Software for 'Omic' Data Analysis and Visualization

# Open-Source Software for 'Omic' Data Analysis and Visualization

## Documentation for package ‘OmicNavigator’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

OmicNavigator-package | OmicNavigator
addAnnotations | Add annotations
addAssays | Add assays
addBarcodes | Add barcode plot metadata
addEnrichments | Add enrichment results
addEnrichmentsLinkouts | Add linkouts to external resources in the enrichments table
addFeatures | Add feature metadata
addMapping | Add mapping object
addMetaAssays | Add metaAssays
addMetaFeatures | Add meta-feature metadata
addMetaFeaturesLinkouts | Add linkouts to external resources in the metaFeatures table
addModels | Add models
addObjects | Add objects
addOverlaps | Add overlaps between annotation gene sets
addPlots | Add custom plotting functions
addReports | Add reports
addResults | Add inference results
addResultsLinkouts | Add linkouts to external resources in the results table
addSamples | Add sample metadata
addTests | Add tests
basal.vs.lp | basal.vs.lp from Bioconductor workflow RNAseq123
basal.vs.ml | basal.vs.ml from Bioconductor workflow RNAseq123
cam.BasalvsLP | cam.BasalvsLP from Bioconductor workflow RNAseq123
cam.BasalvsML | cam.BasalvsML from Bioconductor workflow RNAseq123
combineStudies | Combine two or more studies
createStudy | Create a study
exportStudy | Export a study
getAnnotations | Get annotations from a study
getAssays | Get assays from a study
getBarcodeData | Get data for barcode and violin plots
getBarcodes | Get barcodes from a study
getEnrichments | Get enrichments from a study
getEnrichmentsAnnotations | Get the annotations for the enrichments of an installed OmicNavigator study
getEnrichmentsIntersection | getEnrichmentsIntersection
getEnrichmentsLinkouts | Get enrichments table linkouts from a study
getEnrichmentsModels | Get the models for the enrichments of an installed OmicNavigator study
getEnrichmentsNetwork | Get enrichments network from a study
getEnrichmentsStudies | Get installed OmicNavigator studies that have enrichments
getEnrichmentsTable | Get enrichments table from a study
getEnrichmentsUpset | getEnrichmentsUpset
getFavicons | Get favicon URLs for table linkouts
getFeatures | Get features from a study
getInstalledStudies | Get installed OmicNavigator studies
getLinkFeatures | Get the shared features in a network link
getMapping | Get mapping object from a study
getMetaAssays | Get metaAssays from a study
getMetaFeatures | Get metaFeatures from a study
getMetaFeaturesLinkouts | Get metaFeatures table linkouts from a study
getMetaFeaturesTable | Get metaFeatures for a given feature
getModels | Get models from a study
getNodeFeatures | Get the features in a network node
getObjects | Get objects from a study
getOverlaps | Get overlaps from a study
getPackageVersion | Get version of OmicNavigator package
getPlots | Get plots from a study
getPlottingData | Get plotting data from an OmicNavigator study
getReportLink | Get link to report
getReports | Get reports from a study
getResults | Get results from a study
getResultsIntersection | getResultsIntersection
getResultsLinkouts | Get results table linkouts from a study
getResultsModels | Get the models for the results of an installed OmicNavigator study
getResultsStudies | Get installed OmicNavigator studies that have results
getResultsTable | Get results table from a study
getResultsTests | Get the tests for the results of an installed OmicNavigator study
getResultsUpset | getResultsUpset
getSamples | Get samples from a study
getStudyMeta | Get study metadata
getTests | Get tests from a study
getUpsetCols | getUpsetCols
group | group from Bioconductor workflow RNAseq123
importStudy | Import a study package
installApp | Install the OmicNavigator web app
installStudy | Install a study as an R package
lane | lane from Bioconductor workflow RNAseq123
lcpm | lcpm from Bioconductor workflow RNAseq123
Mm.c2 | Mm.c2 from Bioconductor workflow RNAseq123
OmicNavigator | OmicNavigator
plotStudy | Invoke a custom plotting function
removeStudy | Remove an installed study R package
samplenames | samplenames from Bioconductor workflow RNAseq123
startApp | Start app on local machine
summary.onStudy | Summarize elements of OmicNavigator study
validateStudy | Validate a study