Reduced dimension plots
                        Plot specific reduced dimensions
SCESet                  The "Single Cell Expression Set" (SCESet) class
arrange                 Arrange columns (cells) of a
                        SingleCellExperiment object
bootstraps              Accessor and replacement for bootstrap results
                        in a 'SingleCellExperiment' object
calcIsExprs             Calculate which features are expressed in which
                        cells using a threshold on observed counts,
                        transcripts-per-million, counts-per-million,
                        FPKM, or defined expression levels.
calculateAverage        Calculate average counts, adjusting for size
                        factors or library size
calculateCPM            Calculate counts per million (CPM)
calculateFPKM           Calculate fragments per kilobase of exon per
                        million reads mapped (FPKM)
calculateQCMetrics      Calculate QC metrics
calculateTPM            Calculate transcripts-per-million (TPM)
centreSizeFactors       Centre size factors at unity
filter                  Return 'SingleCellExperiment' with cells
                        matching conditions.
getBMFeatureAnnos       Get feature annotation information from Biomart
getExplanatoryPCs       Estimate the percentage of variance explained
                        for each gene.
getVarianceExplained    Estimate the percentage of variance explained
                        for each gene.
isOutlier               Identify outlier values
librarySizeFactors      Compute library size factors
multiplot               Multiple plot function for ggplot2 plots
mutate                  Add new variables to 'colData(object)'.
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               Normalise a SingleCellExperiment object using
                        pre-computed size factors
normalizeCounts         Divide columns of a count matrix by the size
                        factors
plotColData             Plot column metadata
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
plotQC                  Produce QC diagnostic plots
plotRLE                 Plot a relative log expression (RLE) plot
plotReducedDim          Plot reduced dimensions
plotRowData             Plot row metadata
plotScater              Plot an overview of expression for each cell
readSparseCounts        Read sparse count matrix from file
readTxResults           Read transcript quantification data
rename                  Rename variables of 'colData(object)'.
runDiffusionMap         Create a diffusion map from cell-level data
runMDS                  Perform MDS on cell-level data
runPCA                  Perform PCA on cell-level data
runTSNE                 Perform t-SNE on cell-level data
runUMAP                 Perform UMAP on cell-level data
sc_example_cell_info    Cell information for the small example
                        single-cell counts dataset to demonstrate
                        capabilities of scater
sc_example_counts       A small example of single-cell counts dataset
                        to demonstrate capabilities of scater
scater-package          Single-cell analysis toolkit for expression in
                        R
scater-plot-args        General visualization parameters
scater-vis-var          Variable selection for visualization
sumCountsAcrossFeatures
                        Sum counts across a feature set
summariseExprsAcrossFeatures
                        Summarise expression values across feature
uniquifyFeatureNames    Make feature names unique
updateSCESet            Convert an SCESet object to a
                        SingleCellExperiment object
