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 |
plotDiffHeatmap | Plot differential heatmap |
plotDR | Plot reduced dimensions |
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' |
SCE-accessors | 'SingleCellExperiment' accessors |
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