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Bioinformatics. 2020 Feb 12. pii: btaa091. doi: 10.1093/bioinformatics/btaa091. [Epub ahead of print]

ShinySOM: Graphical SOM-based analysis of single-cell cytometry data.

Author information

1
IOCB of the CAS, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.
2
Department of Software Engineering, MFF UK, Malostranské náměstí 25, Praha 2, Czech Republic.
3
Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic.
4
Childhood Leukaemia Investigation Prague (CLIP), 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.

Abstract

SUMMARY:

ShinySOM offers a user-friendly interface for reproducible, high-throughput analysis of high-dimensional flow and mass cytometry data guided by self-organizing maps. The software implements a FlowSOM-style workflow, with improvements in performance, visualizations and data dissection possibilities. The outputs of the analysis include precise statistical information about the dissected samples, and R-compatible metadata useful for batch processing of large sample volumes.

AVAILABILITY AND IMPLEMENTATION:

ShinySOM is free and open-source, available online at gitlab.com/exaexa/ShinySOM.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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