| .bindCellularBarcodes |
Source code
|
| .cellularBarcodesList |
Source code
|
| .isAggregate |
Source code
|
| .isSanitizedMarkers |
Source code
|
| .minMax |
Source code
|
| .minimalAxis |
Source code
|
| .new.SingleCellExperiment |
Source code
|
| .paddedCount |
Source code
|
| .percentAbove |
Source code
|
| .plotFeatureReduction |
Source code
|
| .plotMarkerReduction |
Source code
|
| .plotQCMetric |
Source code
|
| .plotQCScatterplot |
Source code
|
| .plotReadsPerCellBoxplot |
Source code
|
| .plotReadsPerCellECDF |
Source code
|
| .plotReadsPerCellHistogram |
Source code
|
| .plotReadsPerCellRidgeline |
Source code
|
| .plotReadsPerCellViolin |
Source code
|
| .plotReducedDims |
Source code
|
| .proportionalReadsPerCell |
Source code
|
| .readSparseCounts |
Source code
|
| .reducedDims |
Source code
|
| .sparseCountsList |
Source code
|
| .zinbwave |
Source code
|
| .zinbwave.DESeq2 |
Source code
|
| .zinbwave.edgeR |
Source code
|
| .zingeR.DESeq2 |
Source code
|
| .zingeR.edgeR |
Source code
|
| [,bcbioSingleCell,ANY,ANY,ANY-method |
Man page
|
| aggregateReplicates |
Man page
|
| aggregateReplicates,bcbioSingleCell-method |
Man page
|
| all_markers_small |
Man page
|
| as |
Man page
|
| assay,seurat,ANY-method |
Man page
|
| barcodeRanksPerSample |
Man page
Man page
|
| barcodeRanksPerSample,SingleCellExperiment-method |
Man page
|
| barcodeRanksPerSample,seurat-method |
Man page
|
| bcbio |
Man page
|
| bcbio,seurat-method |
Man page
|
| bcbio<-,seurat-method |
Man page
|
| bcbioSingleCell |
Man page
Source code
|
| bcbioSingleCell-class |
Man page
|
| bcbioSingleCell-package |
Man page
|
| calculateMetrics |
Man page
Source code
|
| cell2sample |
Man page
Man page
|
| cell2sample,SingleCellExperiment-method |
Man page
|
| cell2sample,seurat-method |
Man page
|
| cellCountsPerCluster |
Man page
Man page
|
| cellCountsPerCluster,SingleCellExperiment-method |
Man page
|
| cellCountsPerCluster,seurat-method |
Man page
|
| cellCycleMarkers |
Man page
|
| cellTypeMarkers |
Man page
|
| cellTypesPerCluster |
Man page
Man page
|
| cellTypesPerCluster,grouped_df-method |
Man page
|
| cellranger_small |
Man page
|
| clusterCellCountsPerSample |
Man page
Man page
|
| clusterCellCountsPerSample,SingleCellExperiment-method |
Man page
|
| clusterCellCountsPerSample,seurat-method |
Man page
|
| coerce |
Man page
|
| coerce-SingleCellExperiment-seurat |
Man page
|
| coerce-seurat-SingleCellExperiment |
Man page
|
| colData,seurat-method |
Man page
|
| colnames,seurat-method |
Man page
|
| counts,seurat-method |
Man page
|
| darkTheme |
Man page
Source code
|
| defunct |
Man page
|
| deprecated |
Man page
|
| diffExp |
Man page
Man page
|
| diffExp,SingleCellExperiment-method |
Man page
|
| diffExp,seurat-method |
Man page
|
| extract |
Man page
|
| fetchData |
Man page
|
| fetchGeneData |
Man page
|
| fetchGeneData,SingleCellExperiment-method |
Man page
|
| fetchGeneData,seurat-method |
Man page
|
| fetchPCAData |
Man page
|
| fetchPCAData,SingleCellExperiment-method |
Man page
|
| fetchPCAData,seurat-method |
Man page
|
| fetchTSNEData |
Man page
|
| fetchTSNEData,SingleCellExperiment-method |
Man page
|
| fetchTSNEData,seurat-method |
Man page
|
| fetchTSNEExpressionData |
Man page
|
| fetchTSNEExpressionData,SingleCellExperiment-method |
Man page
|
| fetchTSNEExpressionData,seurat-method |
Man page
|
| fetchUMAPData |
Man page
|
| fetchUMAPData,SingleCellExperiment-method |
Man page
|
| fetchUMAPData,seurat-method |
Man page
|
| fetchUMAPExpressionData |
Man page
|
| fetchUMAPExpressionData,SingleCellExperiment-method |
Man page
|
| fetchUMAPExpressionData,seurat-method |
Man page
|
| filterCells |
Man page
Man page
|
| filterCells,SingleCellExperiment-method |
Man page
|
| gene2symbol,seurat-method |
Man page
|
| general |
Man page
|
| ggplot |
Man page
|
| glimpse |
Man page
|
| indrops_small |
Man page
|
| inferno |
Man page
|
| inflectionPoint |
Man page
Source code
|
| interestingGroups,seurat-method |
Man page
|
| interestingGroups<-,seurat,character-method |
Man page
|
| knownMarkersDetected |
Man page
Man page
|
| knownMarkersDetected,grouped_df-method |
Man page
|
| known_markers_small |
Man page
|
| loadCellRanger |
Man page
Source code
|
| loadSingleCell |
Man page
Source code
|
| loadSingleCellRun |
Man page
Source code
|
| mapCellsToSamples |
Man page
Source code
|
| metadata,seurat-method |
Man page
|
| metadata<-,seurat-method |
Man page
|
| metrics |
Man page
|
| metrics,SingleCellExperiment-method |
Man page
|
| metrics,dgCMatrix-method |
Man page
|
| metrics,dgTMatrix-method |
Man page
|
| metrics,matrix-method |
Man page
|
| metrics,seurat-method |
Man page
|
| metricsPerSample |
Man page
Man page
|
| metricsPerSample,SingleCellExperiment-method |
Man page
|
| metricsPerSample,seurat-method |
Man page
|
| pcCutoff |
Man page
Source code
|
| plotBarcodeRanks |
Man page
Man page
|
| plotBarcodeRanks,SingleCellExperiment-method |
Man page
|
| plotBarcodeRanks,seurat-method |
Man page
|
| plotCellCounts |
Man page
Man page
|
| plotCellCounts,SingleCellExperiment-method |
Man page
|
| plotCellCounts,seurat-method |
Man page
|
| plotCellTypesPerCluster |
Man page
Man page
|
| plotCellTypesPerCluster,seurat-method |
Man page
|
| plotClusters |
Man page
Source code
|
| plotCumulativeUMIsPerCell |
Man page
Source code
|
| plotDimensionalReduction |
Man page
|
| plotDot |
Man page
|
| plotDot,SingleCellExperiment-method |
Man page
|
| plotDot,seurat-method |
Man page
|
| plotFeature |
Man page
|
| plotFeatureTSNE |
Man page
|
| plotFeatureTSNE,SingleCellExperiment-method |
Man page
|
| plotFeatureTSNE,seurat-method |
Man page
|
| plotFeatureUMAP |
Man page
|
| plotFeatureUMAP,SingleCellExperiment-method |
Man page
|
| plotFeatureUMAP,seurat-method |
Man page
|
| plotFeatures |
Man page
Source code
|
| plotGene |
Man page
|
| plotGene,SingleCellExperiment-method |
Man page
|
| plotGene,seurat-method |
Man page
|
| plotGenesPerCell |
Man page
Man page
|
| plotGenesPerCell,SingleCellExperiment-method |
Man page
|
| plotGenesPerCell,seurat-method |
Man page
|
| plotKnownMarkers |
Man page
Source code
|
| plotKnownMarkersDetected |
Man page
|
| plotKnownMarkersDetected,SingleCellExperiment-method |
Man page
|
| plotKnownMarkersDetected,seurat-method |
Man page
|
| plotMarker |
Man page
Man page
Source code
|
| plotMarkerTSNE |
Man page
|
| plotMarkerTSNE,SingleCellExperiment-method |
Man page
|
| plotMarkerTSNE,seurat-method |
Man page
|
| plotMarkerUMAP |
Man page
|
| plotMarkerUMAP,SingleCellExperiment-method |
Man page
|
| plotMarkerUMAP,seurat-method |
Man page
|
| plotMarkers |
Man page
Source code
|
| plotMitoRatio |
Man page
Man page
|
| plotMitoRatio,SingleCellExperiment-method |
Man page
|
| plotMitoRatio,seurat-method |
Man page
|
| plotMitoVsCoding |
Man page
Man page
|
| plotMitoVsCoding,SingleCellExperiment-method |
Man page
|
| plotMitoVsCoding,seurat-method |
Man page
|
| plotNovelty |
Man page
Man page
|
| plotNovelty,SingleCellExperiment-method |
Man page
|
| plotNovelty,seurat-method |
Man page
|
| plotPCA,SingleCellExperiment-method |
Man page
|
| plotPCA,seurat-method |
Man page
|
| plotPCElbow |
Man page
Man page
|
| plotPCElbow,seurat-method |
Man page
|
| plotQC |
Man page
|
| plotQC,SingleCellExperiment-method |
Man page
|
| plotQC,seurat-method |
Man page
|
| plotReadsPerCell |
Man page
Man page
|
| plotReadsPerCell,bcbioSingleCell-method |
Man page
|
| plotTSNE |
Man page
|
| plotTSNE,SingleCellExperiment-method |
Man page
|
| plotTSNE,seurat-method |
Man page
|
| plotTSNEExpressionData |
Man page
Source code
|
| plotTopMarkers |
Man page
|
| plotTopMarkers,SingleCellExperiment-method |
Man page
|
| plotTopMarkers,seurat-method |
Man page
|
| plotUMAP |
Man page
|
| plotUMAP,SingleCellExperiment-method |
Man page
|
| plotUMAP,seurat-method |
Man page
|
| plotUMIsPerCell |
Man page
Man page
|
| plotUMIsPerCell,SingleCellExperiment-method |
Man page
|
| plotUMIsPerCell,seurat-method |
Man page
|
| plotUMIsVsGenes |
Man page
Man page
|
| plotUMIsVsGenes,SingleCellExperiment-method |
Man page
|
| plotUMIsVsGenes,seurat-method |
Man page
|
| plotViolin |
Man page
|
| plotViolin,SingleCellExperiment-method |
Man page
|
| plotViolin,seurat-method |
Man page
|
| plotZerosVsDepth |
Man page
Man page
|
| plotZerosVsDepth,SingleCellExperiment-method |
Man page
|
| plotZerosVsDepth,seurat-method |
Man page
|
| prepareSingleCellTemplate |
Man page
Source code
|
| pull |
Man page
|
| quantileHeatmap |
Man page
Source code
|
| readCellRanger |
Man page
Source code
|
| readCellTypeMarkers |
Man page
Source code
|
| readCellTypeMarkersFile |
Man page
Source code
|
| readMarkers |
Man page
Source code
|
| readMarkersFile |
Man page
Source code
|
| reexports |
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
|
| rowData,seurat-method |
Man page
|
| rowRanges,seurat-method |
Man page
|
| rownames,seurat-method |
Man page
|
| sampleData |
Man page
|
| sampleData,SingleCellExperiment-method |
Man page
|
| sampleData,seurat-method |
Man page
|
| sampleData<-,SingleCellExperiment,DataFrame-method |
Man page
|
| sampleData<-,seurat,DataFrame-method |
Man page
|
| sampleNames,seurat-method |
Man page
|
| sanitizeMarkers |
Man page
Man page
|
| sanitizeMarkers,seurat-method |
Man page
|
| scale_color_gradient |
Man page
|
| scale_color_hue |
Man page
|
| scale_color_viridis |
Man page
|
| scale_colour_gradient |
Man page
|
| scale_colour_gradientn |
Man page
|
| scale_colour_hue |
Man page
|
| scale_colour_viridis |
Man page
|
| scale_fill_hue |
Man page
|
| scale_fill_viridis |
Man page
|
| selectSamples |
Man page
|
| selectSamples,SingleCellExperiment-method |
Man page
|
| seurat-SingleCellExperiment |
Man page
|
| seurat_small |
Man page
|
| show |
Man page
|
| show,bcbioSingleCell-method |
Man page
|
| subsetPerSample |
Man page
Man page
|
| subsetPerSample,bcbioSingleCell-method |
Man page
|
| topBarcodes |
Man page
Man page
|
| topBarcodes,SingleCellExperiment-method |
Man page
|
| topBarcodes,seurat-method |
Man page
|
| topMarkers |
Man page
Man page
|
| topMarkers,grouped_df-method |
Man page
|
| updateObject |
Man page
|
| updateObject,bcbioSingleCell-method |
Man page
|
| viridis |
Man page
|
