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Open Access Software

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

Additional files

Additional file 1:

A copy of the flowClust package. The zip file contains the source code of the flowClust package (version 2.2.0) as a gzipped tarball for direct installation into R from a command-line interface. This current release is also available from Bioconductor at webcite.

Format: ZIP Size: 262KB Download file

Open Data

Additional file 2:

A copy of the GvHD data file used in this article. The zip file contains the data file in FCS format used in the GvHD analysis. Interested readers may go to webcite for a complete set of data files for the GvHD study [40].

Format: ZIP Size: 129KB Download file

Open Data

Additional file 3:

A graph with two BIC curves corresponding to the settings with a common λ and cluster-specific λ respectively for the first-stage cluster analysis. Little difference in the BIC values between the two settings is observed. In accordance with the principle of parsimony which favors a simpler model, we opt for the default setting here.

Format: PDF Size: 5KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Result summary of the first-stage analysis with four clusters of the GvHD data. The rule used to identify outliers is 95% quantile. 133 points (1.03%) are called outliers.

Format: TXT Size: 1KB Download file

Open Data

Additional file 5:

Code to produce the plots in this article. R code to produce the plots in the GvHD analysis.

Format: R Size: 1KB Download file

Open Data