API for roryk/bcbioSinglecell
Single-Cell RNA-Seq Utilities

Global functions
[,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
bindCellularBarcodes Source code
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
cellularBarcodesList Source code
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
minMax Source code
minimalAxis Source code
new.SingleCellExperiment Source code
paddedCount Source code
pcCutoff Man page Source code
percentAbove 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
plotFeatureReduction Source code
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
plotMarkerReduction 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
plotQCMetric Source code
plotQCScatterplot Source code
plotReadsPerCell Man page Man page
plotReadsPerCell,bcbioSingleCell-method Man page
plotReadsPerCellBoxplot Source code
plotReadsPerCellECDF Source code
plotReadsPerCellHistogram Source code
plotReadsPerCellRidgeline Source code
plotReadsPerCellViolin Source code
plotReducedDims Source code
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
proportionalReadsPerCell 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
readSparseCounts Source code
reducedDims 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
sAggregate Source code
sSanitizedMarkers Source code
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
sparseCountsList Source code
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
zinbwave Source code
zinbwave.DESeq2 Source code
zinbwave.edgeR Source code
zingeR.DESeq2 Source code
zingeR.edgeR Source code
roryk/bcbioSinglecell documentation built on July 19, 2018, 3:33 a.m.