ShinySOM: graphical SOM-based analysis of single-cell cytometry data

Miroslav Kratochvíl; David Bednárek; Tomáš Sieger; Karel Fišer; Jiří Vondrášek

doi:10.1093/bioinformatics/btaa091

ShinySOM: graphical SOM-based analysis of single-cell cytometry data

Bioinformatics. 2020 May 1;36(10):3288-3289. doi: 10.1093/bioinformatics/btaa091.

Authors

Miroslav Kratochvíl^{1

2}, David Bednárek², Tomáš Sieger³, Karel Fišer⁴, Jiří Vondrášek¹

Affiliations

¹ Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Praha 6, Czech Republic.
² Department of Software Engineering, MFF, Charles University, 118 00 Prague, Czech Republic.
³ Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, 121 35 Prague 2, Czech Republic.
⁴ Childhood Leukaemia Investigation Prague (CLIP), 2nd Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Praha 5, 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 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Metadata
Software*
Workflow