# Cytometry dATa anALYSis Tools

## Documentation for package ‘CATALYST’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adaptSpillmat | Adapt spillover matrix
applyCutoffs | Single-cell debarcoding (2)
assignPrelim | Single-cell debarcoding (1)
channels | 'SingleCellExperiment' accessors
channels-method | 'SingleCellExperiment' accessors
clrDR | DR plot on CLR of proportions
cluster | 'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering
cluster_codes | 'SingleCellExperiment' accessors
cluster_codes-method | 'SingleCellExperiment' accessors
cluster_ids | 'SingleCellExperiment' accessors
cluster_ids-method | 'SingleCellExperiment' accessors
compCytof | Compensate CyTOF data
computeSpillmat | Compute spillover matrix
data | Example data sets
delta_area | 'SingleCellExperiment' accessors
delta_area-method | 'SingleCellExperiment' accessors
ei | 'SingleCellExperiment' accessors
ei-method | 'SingleCellExperiment' accessors
estCutoffs | Estimation of distance separation cutoffs
extractClusters | Extract clusters from a 'SingleCellExperiment'
filterSCE | 'SingleCellExperiment' filtering
guessPanel | Guess parameter panel
isotope_list | Example data sets
marker_classes | 'SingleCellExperiment' accessors
marker_classes-method | 'SingleCellExperiment' accessors
mergeClusters | Manual cluster merging
merging_table | Example data sets
mp_cells | Example data sets
normCytof | Bead-based normalization
n_cells | 'SingleCellExperiment' accessors
n_cells-method | 'SingleCellExperiment' accessors
PBMC_fs | Example data sets
PBMC_md | Example data sets
PBMC_panel | Example data sets
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
raw_data | Example data sets
runDR | Dimension reduction
sample_ff | Example data sets
sample_ids | 'SingleCellExperiment' accessors
sample_ids-method | 'SingleCellExperiment' accessors
sample_key | Example data sets
SCE-accessors | 'SingleCellExperiment' accessors
sce2fcs | SCE to 'flowFrame/Set'
ss_exp | Example data sets
state_markers | 'SingleCellExperiment' accessors
state_markers-method | 'SingleCellExperiment' accessors
type_markers | 'SingleCellExperiment' accessors
type_markers-method | 'SingleCellExperiment' accessors