FlowSOM protocols

FlowSOM computational protocol

FlowSOM specifications


Unique identifier OMICS_11053
Name FlowSOM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data FCS files
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.12.0
Stability Stable
BiocGenerics, BiocStyle, R(>=3.2), igraph, XML, flowCore, tsne, ConsensusClusterPlus, flowUtils
Maintained Yes


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  • person_outline Sofie Van Gassen <>

Publication for FlowSOM

FlowSOM IN pipeline

PMCID: 5459756
PMID: 28343983
DOI: 10.1016/j.stem.2017.02.014

[…] events affected by technical variation, such as abrupt flow rate fluctuations (monaco et al., 2016). gating was performed in flowjo v.10.1 (flowjo, llc). subsequent analysis was performed using flowsom (v1.2.0), an r bioconductor package that uses self-organizing maps for dimensional reduction visualization of flow cytometry data (van gassen et al., 2015). all data was scaled and logicle […]

FlowSOM institution(s)
Department of Information Technology, Ghent University, iMinds, Ghent, Belgium; Inflammation Research Center, VIB, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium

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