Registration Open for Bioc2024 July 24-26


Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Bioconductor version: Release (3.19)

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Author: Greg Finak, Mike Jiang

Maintainer: Greg Finak <greg at>, Mike Jiang <mike at>

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


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:

flowWorkspace Introduction: A Package to store and maninpulate gated flow data HTML R Script
How to merge GatingSets HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 4.16.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License AGPL-3.0-only
Depends R (>= 3.5.0)
Imports Biobase, BiocGenerics, cytolib(>= 2.13.1), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales (>= 1.3.0), matrixStats, RProtoBufLib, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4), DelayedArray, S4Vectors
System Requirements GNU make, C++11
See More
Suggests testthat, flowWorkspaceData(>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto
Linking To cpp11, BH (>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib(>= 2.3.7), Rhdf5lib
Depends On Me flowGate, ggcyto, highthroughputassays
Imports Me CytoML, flowStats, PeacoQC
Suggests Me CATALYST, COMPASS, flowClust, flowCore, FlowSOM
Links To Me CytoML
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package flowWorkspace_4.16.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) flowWorkspace_4.16.0.tgz
macOS Binary (arm64) flowWorkspace_4.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats