Computational Cytometry

and Bioinformatics

Recent Posts

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DataPackageR is used to reproducibly process raw data into packaged, analysis-ready data sets.


Open-source data-driven gating for cytometry.

Standardizing Cytometry Data Analysis

Results of the FlowCAP Lyoplate Challenge.


Developed and supported by our group

  • openCyto A framework for computational analysis of cytometry data.
  • flowWorkspace Import gated cytometry data from FlowJo into R/Bioconductor.
  • ggcyto Grammar of graphics for cytometry data visualization.
  • CytoML Cross-platform sharing of analyzed cytometry data.
  • DataPackageR Framework for packaging and sharing analysis-ready data sets in a reproducible way.
  • COMPASS Combinatorial polyfunctionality anslysis of single cells.
  • MIMOSA Mixture models for single cell assays.
  • MAST Modeling and statistical analysis of single cell transcriptomics.

Selected Publications

COMPASS identifies T-cell subsets correlated with clinical outcomes

PDF Source Document

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

PDF Code Project Source Document

Thinking outside the gate: single-cell assessments in multiple dimensions

PDF Source Document

Recent Publications

More Publications

. Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis. Sci Rep, (7), 1, pp. 11948, 2017.


. Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells. PLoS Pathog., (13), 6, pp. e1006445, 2017.


. DNA Priming Increases Frequency of T-Cell Responses to a Vesicular Stomatitis Virus HIV Vaccine with Specific Enhancement of CD8+ T-Cell Responses by Interleukin-12 Plasmid DNA. Clin. Vaccine Immunol., (24), 11, 2017.


. Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial. J. Infect. Dis., (215), 9, pp. 1376–1385, 2017.


. Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial. Lancet, (390), 10101, pp. 1511–1520, 2017.


Recent & Upcoming Talks

Translational Bioinformatics for Cytometry
Jun 6, 2018 12:30 PM