basetheme               Package-wide, non-user function used to set a
                        base 'ggplot2' theme.
clusKNN                 A wrapper function for 'Seurat"s
                        'FindNeighbors' and 'FindClusters'.
contourPlot             Draw a contour plot, typically relating to
                        co-ordinates of a 2-dimensional reduction /
                        embedding, typically contained within a
                        'SingleCellExperiment' object.
downsampleByVar         Downsample an input data-frame or matrix based
                        on variance.
importData              Import a data-frame or matrix, and associated
                        metadata, to a 'SingleCellExperiment' object.
markerEnrichment        Find enriched markers per identified cluster
                        and calculate cluster abundances across these
                        for samples and metadata variables.
markerExpression        Highlight the individual marker expression
                        profile across a 2-dimensional reduction /
                        embedding, typically contained within a
                        'SingleCellExperiment' object. By default, this
                        function plots the expression profile of 6
                        randomly-selected markers from your data.
markerExpressionPerCluster
                        Generate box-and-whisker plots illustrating
                        marker expression per k-NN identified cluster.
                        By default, 5 randomly-selected clusters are
                        selected, and the expression profiles of 10
                        randomly-selected markers are plot across
                        these.
metadataPlot            Colour shade a 2-dimensional reduction /
                        embedding based on metadata, typically
                        contained within a 'SingleCellExperiment'
                        object.
performUMAP             Perform UMAP on an input data-frame or matrix,
                        or 'SingleCellExperiment' object, using the
                        basic R implementation of UMAP.
plotClusters            Highlight cell-to-cluster assignments across a
                        2-dimensional reduction / embedding.
plotSignatures          Find enriched markers per identified cluster
                        and visualise these as a custom corrplot.
processFCS              Input, filter, normalise, and transform FCS
                        expression data.
