API for cTRAP
Identification of candidate causal perturbations from differential gene expression data
| Global functions | |
|---|---|
| .cmapDataLoaderServer | Source code |
| .cmapDataLoaderUI | Source code |
| .dataPlotterServer | Source code |
| .dataPlotterUI | Source code |
| .datasetComparisonServer | Source code |
| .datasetComparisonUI | Source code |
| .diffExprENCODEloaderServer | Source code |
| .diffExprENCODEloaderUI | Source code |
| .findMatch | Source code |
| .metadataViewerServer | Source code |
| .metadataViewerUI | Source code |
| .plotBubbles | Man page Source code |
| .prepareDT | Source code |
| .prepareEllipsis | Source code |
| .prepareMetadata | Source code |
| .prepareNavPage | Man page Source code |
| .targetingDrugsVSsimilarPerturbationsPlotterServer | Source code |
| .targetingDrugsVSsimilarPerturbationsPlotterUI | Source code |
| ENCODEmetadata | Man page |
| GCT-class | Man page |
| [.perturbationChanges | Man page |
| `[.perturbationChanges` | Source code |
| analyseDrugSetEnrichment | Man page Source code |
| as.table.referenceComparison | Man page Source code |
| cTRAP | Man page |
| calculateCellLineMean | Man page Source code |
| calculateEvenlyDistributedBins | Source code |
| checkColnames | Man page Source code |
| chunkVector | Man page Source code |
| closeOpenHandles | Man page Source code |
| cmapMetadata | Man page |
| cmapPerturbationsCompounds | Man page |
| cmapPerturbationsKD | Man page |
| compareAgainstCMap | Man page |
| compareAgainstReference | Man page Source code |
| compareAgainstReferencePerMethod | Man page Source code |
| compareQuantile | Man page Source code |
| convertENSEMBLtoGeneSymbols | Man page Source code |
| convertToTable | Source code |
| correlateAgainstReference | Man page Source code |
| correlateGEandDrugSensitivity | Source code |
| counts | Man page |
| diffExprStat | Man page |
| dim.perturbationChanges | Man page Source code |
| dimnames.perturbationChanges | Man page Source code |
| downloadENCODEknockdownMetadata | Man page Source code |
| downloadIfNotFound | Man page Source code |
| filterCMapMetadata | Man page Source code |
| findIntersectingCompounds | Man page Source code |
| fix.datatypes | Man page Source code |
| getCMapConditions | Man page Source code |
| getCMapPerturbationTypes | Man page |
| getENCODEcontrols | Man page Source code |
| launchCMapDataLoader | Man page Source code |
| launchDiffExprLoader | Man page Source code |
| launchMetadataViewer | Man page Source code |
| launchResultPlotter | Man page Source code |
| listExpressionDrugSensitivityAssociation | Man page Source code |
| loadCMapCompoundInfo | Source code |
| loadCMapData | Man page Source code |
| loadCMapGeneInfo | Source code |
| loadCMapMetadata | Source code |
| loadCMapZscores | Man page Source code |
| loadCTRPcompoundInfo | Man page Source code |
| loadCTRPdrugSensitivity | Man page Source code |
| loadCTRPgeneExpression | Man page Source code |
| loadDrugDescriptors | Man page Source code |
| loadENCODEsample | Man page |
| loadENCODEsamples | Man page Source code |
| loadExpressionDrugSensitivityAssociation | Man page Source code |
| loadGDSC7cellLineInfo | Man page Source code |
| loadGDSC7compoundInfo | Man page Source code |
| loadGDSC7drugSensitivity | Man page Source code |
| loadGDSC7file | Man page Source code |
| loadGDSC7geneExpression | Man page Source code |
| loadNCI60drugSensitivity | Man page Source code |
| loadNCI60geneExpression | Man page Source code |
| matchStatsWithDrugSetsID | Man page Source code |
| mergeDatasetsBy | Source code |
| parseCMapID | Man page Source code |
| performDifferentialExpression | Man page Source code |
| performGSEA | Man page Source code |
| performGSEAagainstReference | Man page Source code |
| plot.perturbationChanges | Man page Source code |
| plot.referenceComparison | Man page Source code |
| plotComparison | Source code |
| plotDrugSetEnrichment | Man page Source code |
| plotESplot | Man page Source code |
| plotGSEA | Man page Source code |
| plotMetricDistribution | Man page Source code |
| plotPerturbationChanges | Source code |
| plotSingleCorr | Man page Source code |
| plotTargetingDrug | Source code |
| plotTargetingDrugsVSsimilarPerturbations | Man page Source code |
| predictTargetingDrugs | Man page Source code |
| prepareCMapPerturbations | Man page Source code |
| prepareCMapZscores | Source code |
| prepareDrugSets | Man page Source code |
| prepareENCODEgeneExpression | Man page Source code |
| prepareExpressionDrugSensitivityAssociation | Man page Source code |
| prepareGSEAgenesets | Man page Source code |
| prepareGeneInput | Source code |
| prepareLabel | Source code |
| print.similarPerturbations | Man page Source code |
| processByChunks | Man page Source code |
| processCall | Source code |
| processChunk | Source code |
| processIds | Man page Source code |
| processStats | Source code |
| rankColumns | Man page Source code |
| rankSimilarPerturbations | Man page Source code |
| readGctxIds | Man page Source code |
| readGctxMeta | Man page Source code |
| stripStr | Man page Source code |
| subsetToIds | Man page Source code |
