Cytometry dATa anALYSis Tools


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Documentation for package ‘CATALYST’ version 1.12.2

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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
plotClusterHeatmap Plot cluster heatmap
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
plotMedExprs Pseudobulk-level boxplot
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