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 the 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.

Childhood Leukaemia Investigation Prague 2nd Faculty of Medicine Charles University and University Hospital Motol 150 06 Praha 5 Czech Republic

Department of Cybernetics Faculty of Electrical Engineering Czech Technical University Prague 121 35 Prague 2 Czech Republic

Department of Software Engineering MFF Charles University 118 00 Prague Czech Republic

Institute of Organic Chemistry and Biochemistry AS CR 166 10 Praha 6 Czech Republic

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