Function reference
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CellCycleMarkers-class - Cell-cycle markers
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CellCycleMarkers()importCellCycleMarkers() - Cell-cycle markers
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CellTypeMarkers-class - Cell-type markers
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CellTypeMarkers()importCellTypeMarkers() - Cell-type markers
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KnownMarkers-class - Known markers
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aggregate() - Aggregate
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aggregateCellsToSamples() - Aggregate cells to samples
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barcodeRanksPerSample() - Barcode ranks per sample
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cellCountsPerCluster() - Cell counts per cluster
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cellCycleMarkersList - Cell-cycle markers list
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cellToSample() - Cell-to-sample mappings
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cellTypeMarkersList - Cell-type markers list
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cellTypesPerCluster() - Cell types per cluster
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clusters() - Cluster identifiers
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combine() - Combine multiple objects
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convertSampleIdsToNames() - Convert sample identifiers to names
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diffExp() - Differential expression
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diffExpPerCluster() - Differential expression per cluster
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export() - Export data from R
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filterCells() - Filter cells
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findMarkers() - Find cluster-specific marker genes
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geometricMean() - Geometric mean
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indropsSampleIndexCounts() - Get the inDrops sample index counts from i5 FASTQ files
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makeSingleCellExperiment() - Make a SingleCellExperiment object
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mapCellsToSamples() - Map cells to samples
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melt() - Melt data from wide to long format
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metrics()metricsPerSample() - Quality control metrics
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normalize() - Normalize expression using pre-computed size factors
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sampleData()`sampleData<-`() - Sample data
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selectSamples() - Select samples
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show() - Show an object
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subsetPerSample() - Subset per sample
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topCellsPerSample() - Top cells per sample
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zerosVsDepth() - Percentage of zeros vs. library depth