SCESet                  The "Single Cell Expression Set" (SCESet) class
accessors               Additional accessors for the typical elements
                        of a SingleCellExperiment object.
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)
deprecated              Retrieve a representation of gene expression
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 if a cell is an outlier based on a
                        metric
kallisto-wrapper        kallisto wrapper functions
multiplot               Multiple plot function for ggplot2 plots
mutate                  Add new variables to 'colData(object)'.
newSCESet               Create a new SCESet object
nexprs                  Count the number of expressed genes per cell
normaliseExprs          Normalise expression expression levels for an
                        SingleCellExperiment object
normalize               Normalise a SingleCellExperiment object using
                        pre-computed size factors
plotExplanatoryVariables
                        Plot explanatory variables ordered by
                        percentage of phenotypic variance explained
plotExpression          Plot expression values for a set of features
                        (e.g. genes or transcripts)
plotExprsFreqVsMean     Plot frequency of expression against mean
                        expression level
plotExprsVsTxLength     Plot expression against transcript length
plotFeatureData         Plot feature (gene) data from a
                        SingleCellExperiment object
plotHighestExprs        Plot the features with the highest expression
                        values
plotMDS                 Produce a multidimensional scaling plot for a
                        SingleCellExperiment object
plotMetadata            Plot metadata for cells or features
plotPhenoData           Plot cell phenotype data from an
                        SingleCellExperiment object
plotPlatePosition       Plot cells in plate positions
plotQC                  Produce QC diagnostic plots
plotRLE                 Plot a relative log expression (RLE) plot
plotReducedDim          Plot reduced dimension representation of cells
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         Plot a diffusion map for a SingleCellExperiment
                        object
runPCA                  Plot PCA for a SingleCellExperiment object
runTSNE                 Plot t-SNE for an SingleCellExperiment object
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_gui              scater GUI function
summariseExprsAcrossFeatures
                        Summarise expression values across feature
updateSCESet            Convert an SCESet object to a
                        SingleCellExperiment object
