SCE-accessors           'SingleCellExperiment' accessors
adaptSpillmat           Adapt spillover matrix
applyCutoffs            Single-cell debarcoding (2)
assignPrelim            Single-cell debarcoding (1)
clrDR                   DR plot on CLR of proportions
cluster                 'FlowSOM' clustering & 'ConsensusClusterPlus'
                        metaclustering
compCytof               Compensate CyTOF data
computeSpillmat         Compute spillover matrix
data                    Example data sets
estCutoffs              Estimation of distance separation cutoffs
extractClusters         Extract clusters from a 'SingleCellExperiment'
filterSCE               'SingleCellExperiment' filtering
guessPanel              Guess parameter panel
mergeClusters           Manual cluster merging
normCytof               Bead-based normalization
pbMDS                   Pseudobulk-level MDS plot
plotAbundances          Population frequencies across samples &
                        clusters
plotClusterExprs        Plot expression distributions by cluster
plotCodes               tSNE and PCA on SOM codes
plotCounts              Plot cell counts
plotDR                  Plot reduced dimensions
plotDiffHeatmap         Plot differential heatmap
plotEvents              Event plot
plotExprHeatmap         Plot expression heatmap
plotExprs               Expression densities
plotFreqHeatmap         Cluster frequency heatmap
plotMahal               Biaxial plot
plotMultiHeatmap        Multi-panel expression & frequency heatmaps
plotNRS                 Plot non-redundancy scores
plotPbExprs             Pseudobulk-level boxplot
plotScatter             Scatter plot
plotSpillmat            Spillover matrix heatmap
plotYields              Yield plot
prepData                Data preparation
runDR                   Dimension reduction
sce2fcs                 SCE to 'flowFrame/Set'
