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This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see flowWorkspace.

Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

Bioconductor version: 3.1

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>,Mike Jiang <wjiang2 at>

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


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PDF R Script Importing flowJo Workspaces into R
HTML R Script How to merge GatingSets
HTML R Script How to plot gated data
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, FlowCytometry, Preprocessing, Software
Version 3.14.9
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends R (>= 2.16.0), flowCore(>= 1.33.13), flowViz(>= 1.29.27), ncdfFlow(>= 2.13.04), gridExtra
Imports Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, XML, tools, gridExtra, Rgraphviz, data.table, plyr, latticeExtra, Rcpp, RColorBrewer, stringr
LinkingTo Rcpp, BH (>= 1.58.0-1)
Suggests testthat, flowWorkspaceData, RSVGTipsDevice, knitr
SystemRequirements xml2, GNU make
Depends On Me flowStats, openCyto, QUALIFIER
Suggests Me COMPASS, flowCore
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