flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
CONCLUSIONS
flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. The algorithm is based on a sequential bivariate gating approach that generates a set of predefined cell populations. It chooses the best cut-off for individual markers using characteristics of the density distribution. The Supplementary Material is linked to the online version of the manuscript.


METHODS
R source code freely available through BioConductor (http://master.bioconductor.org/packages/devel/bioc/html/flowDensity.html.). Data available from FlowRepository.org (dataset FR-FCM-ZZBW).


BACKGROUND
rbrinkman@bccrc.ca


BACKGROUND
Supplementary data are available at Bioinformatics online.
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Mehrnoush
M
Malek
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Mohammad Jafar
MJ
Taghiyar
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Lauren
L
Chong
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Greg
G
Finak
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Raphael
R
Gottardo
Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
Ryan R
RR
Brinkman
D000465:Algorithms; D015415:Biomarkers; D002468:Cell Physiological Phenomena; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D005434:Flow Cytometry / Q000379:methods*; D006801:Humans; D012984:Software
D015415:Biomarkers