DOI: 10.18129/B9.bioc.flowWorkspace    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see flowWorkspace.

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

Bioconductor version: 3.12

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 <gfinak at fhcrc.org>,Mike Jiang <wjiang2 at fhcrc.org>,Jake Wagner <jpwagner at fhcrc.org>

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


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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:



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


biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 4.2.0
In Bioconductor since BioC 2.9 (R-2.14) (9.5 years)
License file LICENSE
Depends R (>= 3.5.0)
Imports Biobase, BiocGenerics, cytolib(>= 2.1.20), lattice, latticeExtra, XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, Rcpp, scales, matrixStats, RcppParallel, RProtoBufLib, digest, aws.s3, aws.signature, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4)
LinkingTo Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib(>= 2.1.15), Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1)
Suggests testthat, flowWorkspaceData(>= 2.23.2), knitr, ggcyto, parallel, CytoML, openCyto
SystemRequirements GNU make, C++11
Depends On Me ggcyto, highthroughputassays
Imports Me CytoML, flowDensity, FlowSOM, flowStats, ImmuneSpaceR, openCyto, PeacoQC
Suggests Me CATALYST, COMPASS, flowClust, flowCore
Links To Me CytoML
Build Report  

Package Archives

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

Source Package flowWorkspace_4.2.0.tar.gz
Windows Binary flowWorkspace_4.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) flowWorkspace_4.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/flowWorkspace
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/flowWorkspace
Package Short Url https://bioconductor.org/packages/flowWorkspace/
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