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. Author manuscript; available in PMC: 2021 Nov 2.
Published in final edited form as: Methods Enzymol. 2019 Dec 19;632:309–337. doi: 10.1016/bs.mie.2019.11.012

Table 3.

Clustering methods.

Method Environment Description Limitations
PhenoGraph R (included in Cytofkit), Phyton, MATLAB™, FlowJo Exchange plug-in Based on nearest-neighbor graph, followed by definition of communities as interconnected events Number of clusters not customizable Not so fast
ClusterX R (defined in Cytofkit) Based on densities in the tSNE projection map Fast Limited to tSNE ability to define clusters Number of clusters not customizable
FlowSOM R package (included in Cytofkit), FlowJo Exchange plug-in Based in Self-Organization Maps (SOM) follow by hierarchical clustering Very fast Number of clusters customizable For exploratory analysis, hard to determine the number of clusters