FlowSOM protocols

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FlowSOM specifications

Information


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
Requirements
BiocGenerics, BiocStyle, R(>=3.2), igraph, XML, flowCore, tsne, ConsensusClusterPlus, flowUtils
Maintained Yes

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Documentation


Maintainer


  • person_outline Sofie Van Gassen <>

Publication for FlowSOM

FlowSOM in pipeline

2017
PMCID: 5459756
PMID: 28343983
DOI: 10.1016/j.stem.2017.02.014

[…] package that filters events affected by technical variation, such as abrupt flow rate fluctuations (). 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 (). all data was scaled and logicle transformed on import. […]


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FlowSOM in publications

 (9)
PMCID: 5869589
PMID: 29588478
DOI: 10.1038/s41467-018-02977-8

[…] the global perturbation of dc haematopoiesis induced by ikzf1 mutation, an unsupervised phenotypic analysis and enumeration was initially conducted using a member of family b (b5) and a control. the flowsom algorithm was used to cluster, visualise and compare equal numbers of data from the lineage−hla-dr+ (lin−dr+) cd14− gate of a 16-colour flow cytometry panel (supplementary figure , […]

PMCID: 5857569
PMID: 29593710
DOI: 10.3389/fimmu.2018.00380

[…] formulations when mice had been primed with h56 and caf01, but not with h56 alone. the polyfunctional nature of t helper cells was analyzed and visualized with the multidimensional flow cytometry flowsom software, implemented as a package of the r environment. a similar cytokine profile was detected in groups primed with h56 + caf01 and boosted with or without adjuvant, except […]

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

[…] 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 ()., […]

PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] populations based on the expression of all six markers, we divided the cells into populations using automated clustering algorithms (supplementary fig. ). the best clustering was constructed by flowsom, dividing the total γδ thymocyte pool into seven distinct populations that are referred hereafter to as populations a through g (fig. ). these populations were all present in mice from 1 […]

PMCID: 5551572
PMID: 28698286
DOI: 10.1084/jem.20162031

[…] of spleen and silp—without any further pregating—were fed into the dimensionality reduction algorithm t-stochastic neighbor embedding (t-sne), followed by analysis of the combined data sets with flowsom (k = 5). strikingly, the unsupervised clustering separated splenic and silp rorcfm+ ilcs into clearly demarcated cluster sets (). although almost all silp rorcfm+ ilcs grouped together in one […]


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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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