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Table 1 Comparison between other tools and workflows and CytoTree

From: CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data

Computational modules Functions OpenCyto MetaCyto FlowIO FlowCal AutoGate cytofkit diffcyt CytoSOM CyTOF workflow CytoTree
Preprocessing Denisty plot   
Gating  
Concatenation
Normalization
Clustering SOM     
kmeans        
clara          
PhenoGraph        
hclust          
Processing clusters and branches Downsampling        
DR-clusters       
Diff-exp      
Dimensionality reduction PCA        
tSNE        
Diff-maps          
UMAP         
Trajectory Tree         
Analysis Pseudotime          
Inter-state          
  1. DR-clusters dimensionality reduction for clusters, diff-maps diffusion maps, diff-exp differentially expressed markers, inter-state intermediate state analysis
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