FlowIO: Flow cytometry standard conformance testing, editing, and export tool. Issue 8 (15th August 2018)

• Record Type: Journal Article
• Authors: Koblížek, Miroslav; Lebedeva, Anastasia; Fišer, Karel
• Is Part Of: Cytometry. Volume 93:Issue 8(2018)
• Page Start: 848
• Page End: 853
• Publication Date: 2018-08-15
• Subjects: flow cytometry -- FCS -- data standard -- file format -- bioinformatics -- reproducibility in science; Flow cytometry -- Periodicals; Imaging systems in biology -- Periodicals; Imaging systems in medicine -- Periodicals; Diagnostic imaging -- Periodicals; 571.605
• DOI: 10.1002/cyto.a.23563
• Languages: English
• ISSNs: 1552-4922

Abstract

Abstract: The Flow Cytometry Standard (FCS) format is a widely accepted norm for storing Flow Cytometry (FCM) data. Its goal as a standard is to allow FCM data sharing and re‐analysis. Over more than three decades of its existence FCS has evolved into a well‐defined, flexible file format reflecting technical changes in the FCM field. Its flexibility as well as rising numbers of instrument vendors leads to suboptimal implementations of FCS in some cases. Such situations compromise the primary goal of the standard and hinder the ability to reproduce FCM analyses. It is further underlined by rapid rise of advanced FCM analyses, often carried out outside traditional software tools and heavily relying on standard data storage and presentation. We have developed flowIO, an R package which tests FCS file conformance with the standard as defined by International Society for Advancement of Cytometry (ISAC) normative. Along with the package we provide a web based application (also athttp://bioinformin.cesnet.cz/flowIO/ ) allowing user friendly access to the conformance testing as well as FCS file editing and export for further analysis.