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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


No version available



  • person_outline Sofie Van Gassen

Publication for FlowSOM

FlowSOM citations


Ikaros family zinc finger 1 regulates dendritic cell development and function in humans

Nat Commun
PMCID: 5869589
PMID: 29588478
DOI: 10.1038/s41467-018-02977-8
call_split See protocol

[…] nd a travel control were analysed using an 18-channel (16 fluorochromes, 2 light scatter) panel. Compensated FCS files were manually gated (FlowJo 10.1r5, Treestar, Inc.) to export Lin−DR+CD14− cells.FlowSOM 1.7.1 was used for further analysis. From each of the two files, 550 cells were randomly selected. A total of 12 surface markers were used for building the self-organising map (SOM): CD5, CD14 […]


Heterologous Prime Boost Combinations Highlight the Crucial Role of Adjuvant in Priming the Immune System

Front Immunol
PMCID: 5857569
PMID: 29593710
DOI: 10.3389/fimmu.2018.00380
call_split See protocol

[…] lly gated, concatenated within the same immunization group, randomly downsampled to 15,000 cells and exported as uncompensated cells. Data were then compensated, logically transformed and scaled with FlowSOM (). FlowSOM is a package of R, an open-source environment for statistical analysis, computation, and visualization, available as a Bioconductor package. Clustering analysis of data was perform […]


Human dendritic cell subsets: an update

PMCID: 5904714
PMID: 29313948
DOI: 10.1111/imm.12888

[…] f complex populations of leucocytes or ‘deep phenotyping’ of selected lineages. A number of computational flow cytometry tools have been developed to scale and represent high dimensional data such as FlowSOM, tSNE, oneSENSE, and ISOMAP. This approach, rather than sequential manual gating, aids the unbiased mapping and discovery of new cell phenotypes from multiparameter data, including that gener […]


ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

Sci Data
PMCID: 5827693
PMID: 29485622
DOI: 10.1038/sdata.2018.15

[…] k established by the Galaxy Project established in making code freely available to the wider scientific community. The adaptation of the Galaxy framework to host flow analysis tools such as FLOCK and FlowSOM also addresses several data analysis challenges identified by ImmPort users in providing easier file upload, support for high-throughput analysis, and flexibility to integrate new tools (). […]


QFMatch: multidimensional flow and mass cytometry samples alignment

Sci Rep
PMCID: 5818510
PMID: 29459702
DOI: 10.1038/s41598-018-21444-4

[…] performed independently from sample to sample, even quite similar samples may be poorly aligned.Figure 8Joint clustering and matching. This type of approach, including Joint Clustering and Matching,, FlowSOM and ASPIRE, aligns cell populations based on direct modelling of contributions from individual and grouped samples. It can be thus considered as “hierarchical extension of statistical mixture […]


Comparison of CyTOF assays across sites: Results of a six center pilot study

J Immunol Methods
PMCID: 5805584
PMID: 29174717
DOI: 10.1016/j.jim.2017.11.008

[…] tch effect exists between centers. Similarly, calculating a PCA of all samples prepared by each center, highlights that samples are comparable in a high-dimensional setting.Next, SPADE3 and Cytofkit (FlowSOM, ClusterX, and Rphenograph) analyses were performed on the same harmonized MATLAB-normalized files. The same 14 surface markers were used for clustering in both SPADE3 and Cytofkit (see Sectio […]


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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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