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flowClust: a Bioconductor package for automated gating of flow cytometry data

Kenneth Lo1*, Florian Hahne2, Ryan R Brinkman3 and Raphael Gottardo45

Author Affiliations

1 Department of Statistics, University of British Columbia, 333-6356 Agricultural Road, Vancouver, BC, V6T1Z2, Canada

2 Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA

3 Terry Fox Laboratory, BC Cancer Research Center, 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada

4 Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC, H2W 1R7, Canada

5 Département de biochimie, Université de Montreal, 2900, boul Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada

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BMC Bioinformatics 2009, 10:145  doi:10.1186/1471-2105-10-145

Published: 14 May 2009



As a high-throughput technology that offers rapid quantification of multidimensional characteristics for millions of cells, flow cytometry (FCM) is widely used in health research, medical diagnosis and treatment, and vaccine development. Nevertheless, there is an increasing concern about the lack of appropriate software tools to provide an automated analysis platform to parallelize the high-throughput data-generation platform. Currently, to a large extent, FCM data analysis relies on the manual selection of sequential regions in 2-D graphical projections to extract the cell populations of interest. This is a time-consuming task that ignores the high-dimensionality of FCM data.


In view of the aforementioned issues, we have developed an R package called flowClust to automate FCM analysis. flowClust implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation. The package provides the functionality to identify cell populations whilst simultaneously handling the commonly encountered issues of outlier identification and data transformation. It offers various tools to summarize and visualize a wealth of features of the clustering results. In addition, to ensure its convenience of use, flowClust has been adapted for the current FCM data format, and integrated with existing Bioconductor packages dedicated to FCM analysis.


flowClust addresses the issue of a dearth of software that helps automate FCM analysis with a sound theoretical foundation. It tends to give reproducible results, and helps reduce the significant subjectivity and human time cost encountered in FCM analysis. The package contributes to the cytometry community by offering an efficient, automated analysis platform which facilitates the active, ongoing technological advancement.