# Cytometry dATa anALYSis Tools

## Documentation for package ‘CATALYST’ version 1.8.7

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

## Help Pages

A B C D E F G I L M N O P R S T Y misc

## -- A --

adaptSpillmat | Adapt spillover matrix
adaptSpillmat-method | Adapt spillover matrix
applyCutoffs | Single-cell debarcoding (2)
applyCutoffs-method | Single-cell debarcoding (2)
assignPrelim | Single-cell debarcoding (1)
assignPrelim-method | Single-cell debarcoding (1)

## -- B --

bc_ids | Extraction and replacement methods for objects of class 'dbFrame'
bc_ids-method | Extraction and replacement methods for objects of class 'dbFrame'
bc_key | Extraction and replacement methods for objects of class 'dbFrame'
bc_key-method | Extraction and replacement methods for objects of class 'dbFrame'

## -- C --

cluster | FlowSOM clustering & ConsensusClusterPlus metaclustering
cluster-method | FlowSOM clustering & ConsensusClusterPlus metaclustering
cluster_codes | Extraction and replacement methods for objects of class 'daFrame'
cluster_codes-method | Extraction and replacement methods for objects of class 'daFrame'
cluster_ids | Extraction and replacement methods for objects of class 'daFrame'
cluster_ids-method | Extraction and replacement methods for objects of class 'daFrame'
compCytof | Compensate CyTOF data
compCytof-method | Compensate CyTOF data
computeSpillmat | Compute spillover matrix
computeSpillmat-method | Compute spillover matrix
concatFCS | FCS file Concatenation
concatFCS-method | FCS file Concatenation
counts | Extraction and replacement methods for objects of class 'dbFrame'
counts-method | Extraction and replacement methods for objects of class 'dbFrame'

## -- D --

daFrame | Differential analysis frame class
daFrame-class | Differential analysis frame class
daFrame-method | Differential analysis frame class
daFrame-methods | Extraction and replacement methods for objects of class 'daFrame'
data | Example data sets
dbFrame | Debarcoding frame class
dbFrame-class | Debarcoding frame class
dbFrame-methods | Extraction and replacement methods for objects of class 'dbFrame'
deltas | Extraction and replacement methods for objects of class 'dbFrame'
deltas-method | Extraction and replacement methods for objects of class 'dbFrame'

## -- E --

ei | Extraction and replacement methods for objects of class 'daFrame'
ei-method | Extraction and replacement methods for objects of class 'daFrame'
estCutoffs | Estimation of distance separation cutoffs
estCutoffs-method | Estimation of distance separation cutoffs
exprs | Extraction and replacement methods for objects of class 'daFrame'
exprs-method | Extraction and replacement methods for objects of class 'daFrame'
exprs-method | Extraction and replacement methods for objects of class 'dbFrame'
extractClusters | Extract clusters from a 'daFrame'
extractClusters-method | Extract clusters from a 'daFrame'

## -- F --

filter | Filter daFrame
filter-method | Filter daFrame

## -- G --

guessPanel | Guess parameter panel
guessPanel-method | Guess parameter panel

## -- I --

isotope_list | Example data sets

## -- L --

launchGUI | Launch GUI

## -- M --

marker_classes | Extraction and replacement methods for objects of class 'daFrame'
marker_classes-method | Extraction and replacement methods for objects of class 'daFrame'
mergeClusters | Manual cluster merging
mergeClusters-method | Manual cluster merging
merging_table | Example data sets
mhl_cutoff | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff-method | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff<- | Extraction and replacement methods for objects of class 'dbFrame'
mhl_cutoff<--method | Extraction and replacement methods for objects of class 'dbFrame'
mhl_dists | Extraction and replacement methods for objects of class 'dbFrame'
mhl_dists-method | Extraction and replacement methods for objects of class 'dbFrame'
mp_cells | Example data sets

## -- N --

normCytof | Bead-based normalization
normCytof-method | Bead-based normalization
normed_bcs | Extraction and replacement methods for objects of class 'dbFrame'
normed_bcs-method | Extraction and replacement methods for objects of class 'dbFrame'
n_cells | Extraction and replacement methods for objects of class 'daFrame'
n_cells-method | Extraction and replacement methods for objects of class 'daFrame'

## -- O --

outFCS | Write population-wise FCS files
outFCS-method | Write population-wise FCS files
outFrames | Population-wise 'flowFrame's from a 'dbFrame'
outFrames-method | Population-wise 'flowFrame's from a 'dbFrame'

## -- P --

PBMC_fs | Example data sets
PBMC_md | Example data sets
PBMC_panel | Example data sets
plotAbundances | Population frequencies across samples & clusters
plotAbundances-method | Population frequencies across samples & clusters
plotClusterExprs | Plot expression distributions by cluster
plotClusterExprs-method | Plot expression distributions by cluster
plotClusterHeatmap | Plot cluster heatmap
plotClusterHeatmap-method | Plot cluster heatmap
plotCodes | tSNE and PCA on SOM codes
plotCodes-method | tSNE and PCA on SOM codes
plotCounts | Plot cell counts
plotCounts-method | Plot cell counts
plotDiffHeatmap | Plot differential heatmap
plotDiffHeatmap-method | Plot differential heatmap
plotDR | Plot dim. reduction from a 'daFrame'
plotDR-method | Plot dim. reduction from a 'daFrame'
plotEvents | Event plot
plotEvents-method | Event plot
plotExprHeatmap | Plot expression heatmap
plotExprHeatmap-method | Plot expression heatmap
plotExprs | Plot expressions
plotExprs-method | Plot expressions
plotMahal | Biaxial plot
plotMahal-method | Biaxial plot
plotMDS | MDS plot
plotMDS-method | MDS plot
plotMedExprs | Plot median expressions
plotMedExprs-method | Plot median expressions
plotNRS | Plot non-redundancy scores
plotNRS-method | Plot non-redundancy scores
plotSpillmat | Spillover matrix heat map
plotSpillmat-method | Spillover matrix heat map
plotYields | Yield plot
plotYields-method | Yield plot

## -- R --

raw_data | Example data sets
reducedDim-method | Extraction and replacement methods for objects of class 'daFrame'
reducedDimNames-method | Extraction and replacement methods for objects of class 'daFrame'
reducedDimNames<--method | Extraction and replacement methods for objects of class 'daFrame'
reducedDims-method | Extraction and replacement methods for objects of class 'daFrame'
runDR | Perform dim. reduction on a 'daFrame'
runDR-method | Perform dim. reduction on a 'daFrame'

## -- S --

sample_ff | Example data sets
sample_ids | Extraction and replacement methods for objects of class 'daFrame'
sample_ids-method | Extraction and replacement methods for objects of class 'daFrame'
sample_key | Example data sets
sep_cutoffs | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs-method | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs<- | Extraction and replacement methods for objects of class 'dbFrame'
sep_cutoffs<--method | Extraction and replacement methods for objects of class 'dbFrame'
ss_exp | Example data sets
state_markers | Extraction and replacement methods for objects of class 'daFrame'
state_markers-method | Extraction and replacement methods for objects of class 'daFrame'

## -- T --

type_markers | Extraction and replacement methods for objects of class 'daFrame'
type_markers-method | Extraction and replacement methods for objects of class 'daFrame'

## -- Y --

yields | Extraction and replacement methods for objects of class 'dbFrame'
yields-method | Extraction and replacement methods for objects of class 'dbFrame'

## -- misc --

[-method | Extraction and replacement methods for objects of class 'daFrame'