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

BMC Bioinformatics

Table 1 Comparison between other tools and workflows and CytoTree

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										√
Analysis	Inter-state										√

DR-clusters dimensionality reduction for clusters, diff-maps diffusion maps, diff-exp differentially expressed markers, inter-state intermediate state analysis

ISSN: 1471-2105