To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")

In most cases, you don't need to download the package archive at all.

flowWorkspace

Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

Bioconductor version: Release (3.0)

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>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")

Documentation

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

browseVignettes("flowWorkspace")

 

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
Text   INSTALL

Details

biocViews DataImport, DataRepresentation, FlowCytometry, Preprocessing, Software
Version 3.12.04
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 2.16.0), flowCore(>= 1.31.17), flowViz(>= 1.29.27), ncdfFlow(>= 2.11.34), gridExtra
Imports Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, graph, XML, Biobase, IDPmisc, Cairo, tools, gridExtra, Rgraphviz, data.table, plyr, latticeExtra, Rcpp, RColorBrewer
Suggests testthat, flowWorkspaceData, RSVGTipsDevice, knitr
System Requirements
URL
Depends On Me flowStats, openCyto, QUALIFIER
Imports Me QUALIFIER
Suggests Me COMPASS, flowCore

Package Archives

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

Package Source flowWorkspace_3.12.04.tar.gz
Windows Binary flowWorkspace_3.12.04.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) flowWorkspace_3.12.04.tgz
Mac OS X 10.9 (Mavericks) flowWorkspace_3.12.04.tgz
Browse/checkout source (username/password: readonly)
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