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All functions

CellCycleMarkers-class
Cell-cycle markers
CellCycleMarkers() importCellCycleMarkers()
Cell-cycle markers
CellTypeMarkers-class
Cell-type markers
CellTypeMarkers() importCellTypeMarkers()
Cell-type markers
KnownMarkers-class
Known markers
aggregate()
Aggregate
aggregateCellsToSamples()
Aggregate cells to samples
barcodeRanksPerSample()
Barcode ranks per sample
cell2sample()
Cell-to-sample mappings
cellCountsPerCluster()
Cell counts per cluster
cellCycleMarkersList
Cell-cycle markers list
cellTypeMarkersList
Cell-type markers list
cellTypesPerCluster()
Cell types per cluster
clusters()
Cluster identifiers
combine()
Combine multiple objects
convertSampleIDsToNames()
Convert sample identifiers to names
diffExp()
Differential expression
diffExpPerCluster()
Differential expression per cluster
export()
Export
filterCells()
Filter cells
findMarkers()
Find cluster-specific marker genes
geometricMean()
Geometric mean
makeSingleCellExperiment()
Make a SingleCellExperiment object
mapCellsToSamples()
Map cells to samples
melt()
Melt columns into key-value pairs
metrics() metricsPerSample()
Quality control metrics
normalize()
Normalize expression using pre-computed size factors
sampleData() `sampleData<-`()
Sample data
selectSamples()
Select samples
show()
Show an object
subsetPerSample()
Subset per sample
topCellsPerSample()
Top cells per sample
zerosVsDepth()
Percentage of zeros vs. library depth