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
calculatePCA            Perform PCA on expression data
calculateQCMetrics      Calculate QC metrics
calculateTPM            Calculate TPMs
calculateTSNE           Perform t-SNE on cell-level data
calculateUMAP           Perform UMAP on cell-level data
centreSizeFactors       Centre size factors at unity
getExplanatoryPCs       Per-PC variance explained by a variable
getVarianceExplained    Per-gene variance explained by a variable
isOutlier               Identify outlier values
librarySizeFactors      Compute library size factors
logNormCounts           Compute log-normalized expression values
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.
normalize               Normalize a SingleCellExperiment object using
                        pre-computed size factors
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        Per-cell quality control metrics
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
plotExprsFreqVsMean     Plot frequency against mean for each feature
plotExprsVsTxLength     Plot expression against transcript length
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
scater-plot-args        General visualization parameters
scater-red-dim-args     Dimensionality reduction options
sumCountsAcrossCells    Sum counts across sets of cells
sumCountsAcrossFeatures
                        Sum counts across feature sets
uniquifyFeatureNames    Make feature names unique
updateSCESet            Convert an SCESet object to a
                        SingleCellExperiment object
