Reduced dimension plots
                        Plot specific reduced dimensions
SCESet                  The "Single Cell Expression Set" (SCESet) class
addPerCellQC            Add QC to an SE
annotateBMFeatures      Get feature annotation information from Biomart
bootstraps              Accessor and replacement for bootstrap results
                        in a 'SingleCellExperiment' object
calculateAverage        Calculate per-feature average counts
calculateCPM            Calculate counts per million (CPM)
calculateDiffusionMap   Create a diffusion map from cell-level data
calculateFPKM           Calculate FPKMs
calculateMDS            Perform MDS on cell-level data
calculateNMF            Perform NMF on cell-level data
calculatePCA            Perform PCA on expression data
calculateTPM            Calculate TPMs
calculateTSNE           Perform t-SNE on cell-level data
calculateUMAP           Perform UMAP on cell-level data
defunct                 Defunct functions
getExplanatoryPCs       Per-PC variance explained by a variable
getVarianceExplained    Per-gene variance explained by a variable
ggcells                 Create a ggplot from a SingleCellExperiment
isOutlier               Identify outlier values
librarySizeFactors      Compute library size factors
logNormCounts           Compute log-normalized expression values
makePerCellDF           Create a per-cell data.frame from a
                        SingleCellDataFrame
makePerFeatureDF        Create a per-feature data.frame from a
                        SingleCellDataFrame
medianSizeFactors       Compute median-based size factors
mockSCE                 Mock up a SingleCellExperiment
multiplot               Multiple plot function for ggplot2 plots
nexprs                  Count the number of non-zero counts per cell or
                        feature
norm_exprs              Additional accessors for the typical elements
                        of a SingleCellExperiment object.
normalizeCounts         Compute normalized expression values
numDetectedAcrossCells
                        Number of detected expression values per group
                        of cells
numDetectedAcrossFeatures
                        Number of detected expression values per group
                        of features
perCellQCMetrics        Compute per-cell quality control metrics for a
                        count matrix or a SingleCellExperiment.
perFeatureQCMetrics     Per-feature quality control metrics
plotColData             Plot column metadata
plotDots                Create a dot plot of expression values
plotExplanatoryPCs      Plot the explanatory PCs for each variable
plotExplanatoryVariables
                        Plot explanatory variables ordered by
                        percentage of variance explained
plotExpression          Plot expression values for all cells
plotHeatmap             Plot heatmap of gene expression values
plotHighestExprs        Plot the highest expressing features
plotPlatePosition       Plot cells in plate positions
plotRLE                 Plot relative log expression
plotReducedDim          Plot reduced dimensions
plotRowData             Plot row metadata
plotScater              Plot an overview of expression for each cell
quickPerCellQC          Quick cell-level QC
readSparseCounts        Read sparse count matrix from file
retrieveCellInfo        Cell-based data retrieval
retrieveFeatureInfo     Feature-based data retrieval
runColDataPCA           Perform PCA on column metadata
runMultiUMAP            Multi-modal UMAP
scater-plot-args        General visualization parameters
scater-utils            Developer utilities
sumCountsAcrossCells    Aggregate expression values across groups of
                        cells
sumCountsAcrossFeatures
                        Sum counts across feature sets
uniquifyFeatureNames    Make feature names unique
updateSCESet            Convert an SCESet object to a
                        SingleCellExperiment object
