CytoML for cross‐platform cytometry data sharing. Issue 12 (14th December 2018)

• Record Type: Journal Article
• Authors: Finak, Greg; Jiang, Wenxin; Gottardo, Raphael
• Other Names: Terstappen Leon W.M.M. guestEditor.
• Is Part Of: Cytometry. Volume 93:Issue 12(2018)
• Page Start: 1189
• Page End: 1196
• Publication Date: 2018-12-14
• Subjects: standards -- interoperability -- data sharing -- data analysis -- bioinformatics -- R/bioconductor; Flow cytometry -- Periodicals; Imaging systems in biology -- Periodicals; Imaging systems in medicine -- Periodicals; Diagnostic imaging -- Periodicals; 571.605
• DOI: 10.1002/cyto.a.23663
• Languages: English
• ISSNs: 1552-4922

Abstract

Abstract: CytoML is an R/Bioconductor package that enables cross‐platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. Once data are available in R, the data can be further manipulated. For example it can be combined with other computational and analytic approaches, and the results can be exported to FlowJo or Cytobank to be explored by researchers using those platforms. We demonstrate how CytoML and related R packages can be used as a tool to import, modify and export several samples stained with the T cell panel from the FlowCAP IV Lyoplate data set. Once imported, the gating is modified using computational approaches, and exported for visualization in Cytobank and FlowJo. We further show how CytoML can be used to import gated data from a publicly accessible mass cytometry experiment from Cytobank. CytoML is the only tool that allows such sharing of gated cytometry data between researchers working across different platforms, and it will serve as a useful tool for validating and verifying the reproducibility of analyses. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.