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Annotation and analysis of biological dynamical systems using flow cytometry

Bioconductor version: Release (3.19)

This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.

Author: R. Clay Wright [aut, cre], Nick Bolten [aut], Edith Pierre-Jerome [aut]

Maintainer: R. Clay Wright <wright.clay at>

Citation (from within R, enter citation("flowTime")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Steady-state analysis of flow cytometry data HTML R Script
Time course analysis of flow cytometry data HTML R Script
Yeast gating HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, DataImport, FlowCytometry, ImmunoOncology, Software, TimeCourse, Visualization
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.4), flowCore
Imports utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
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Suggests knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto
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Follow Installation instructions to use this package in your R session.

Source Package flowTime_1.28.0.tar.gz
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macOS Binary (x86_64) flowTime_1.28.0.tgz
macOS Binary (arm64) flowTime_1.28.0.tgz
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Source Repository (Developer Access) git clone
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