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 |
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 |
Plot a feature using 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 |