Reduced dimension plots
                        Plot specific reduced dimensions
SCESet                  The "Single Cell Expression Set" (SCESet) class
areSizeFactorsCentred   Check if the size factors are centred at unity
arrange                 Arrange columns (cells) of a
                        SingleCellExperiment object
bootstraps              Accessor and replacement for bootstrap results
                        in a 'SingleCellExperiment' object
calcAverage             Calculate average counts, adjusting for size
                        factors or library size
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.
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
downsampleCounts        Downsample a count matrix
filter                  Return 'SingleCellExperiment' with cells
                        matching conditions.
findImportantPCs        Find most important principal components for a
                        given variable
getBMFeatureAnnos       Get feature annotation information from Biomart
isOutlier               Identify outlier values
kallisto-wrapper        kallisto wrapper functions
librarySizeFactors      Compute library size factors
multiplot               Multiple plot function for ggplot2 plots
mutate                  Add new variables to 'colData(object)'.
nexprs                  Count the number of expressed genes per cell
norm_exprs              Additional accessors for the typical elements
                        of a SingleCellExperiment object.
normalize               Normalise a SingleCellExperiment object using
                        pre-computed size factors
normalizeExprs          Normalise expression levels for a
                        SingleCellExperiment object
plotColData             Plot column metadata
plotExplanatoryVariables
                        Plot explanatory variables ordered by
                        percentage of phenotypic 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
read10xResults          Load in data from 10x experiment
readTxResults           Read transcript quantification data with
                        tximport package
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
salmon-wrapper          Salmon wrapper functions
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
scater_gui              scater GUI function
summariseExprsAcrossFeatures
                        Summarise expression values across feature
uniquifyFeatureNames    Make feature names unique
updateSCESet            Convert an SCESet object to a
                        SingleCellExperiment object
