Open-Source Software for 'Omic' Data Analysis and Visualization
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Documentation for package ‘OmicNavigator’ version 1.15.0
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 |
| addMetaFeatures | Add meta-feature metadata |
| addMetaFeaturesLinkouts | Add linkouts to external resources in the metaFeatures table |
| addModels | Add models |
| 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 |
| getEnrichmentsIntersection | getEnrichmentsIntersection |
| getEnrichmentsLinkouts | Get enrichments table linkouts from a study |
| getEnrichmentsNetwork | Get enrichments network from a study |
| 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 |
| 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 |
| 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 |
| getResultsTable | Get results table from a study |
| getResultsUpset | getResultsUpset |
| getSamples | Get samples from a study |
| 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 |
| listStudies | List available studies and their metadata |
| 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 |