Man pages for CATALYST
Cytometry dATa anALYSis Tools

adaptSpillmatAdapt spillover matrix
applyCutoffsSingle-cell debarcoding (2)
assignPrelimSingle-cell debarcoding (1)
clrDRDR plot on CLR of proportions
cluster'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering
compCytofCompensate CyTOF data
computeSpillmatCompute spillover matrix
dataExample data sets
estCutoffsEstimation of distance separation cutoffs
extractClustersExtract clusters from a 'SingleCellExperiment'
filterSCE'SingleCellExperiment' filtering
guessPanelGuess parameter panel
mergeClustersManual cluster merging
normCytofBead-based normalization
pbMDSPseudobulk-level MDS plot
plotAbundancesPopulation frequencies across samples & clusters
plotClusterExprsPlot expression distributions by cluster
plotClusterHeatmapPlot cluster heatmap
plotCodestSNE and PCA on SOM codes
plotCountsPlot cell counts
plotDiffHeatmapPlot differential heatmap
plotDRPlot reduced dimensions
plotEventsEvent plot
plotExprHeatmapPlot expression heatmap
plotExprsExpression densities
plotFreqHeatmapCluster frequency heatmap
plotMahalBiaxial plot
plotMultiHeatmapMulti-panel expression & frequency heatmaps
plotNRSPlot non-redundancy scores
plotPbExprsPseudobulk-level boxplot
plotScatterScatter plot
plotSpillmatSpillover matrix heatmap
plotYieldsYield plot
prepDataData preparation
runDRDimension reduction
sce2fcsSCE to 'flowFrame/Set'
SCE-accessors'SingleCellExperiment' accessors
CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.