flowWorkspace

DOI: 10.18129/B9.bioc.flowWorkspace    

Infrastructure for representing and interacting with the gated cytometry

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")

Documentation

HTML	R Script	flowWorkspace Introduction: A Package to store and maninpulate gated flow data
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	3.26.9
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 years)
License	Artistic-2.0
Depends	R (>= 2.16.0), flowCore(>= 1.39.9), ncdfFlow(>= 2.19.5)
Imports	Biobase, BiocGenerics, graph, graphics, grDevices, lattice, methods, stats, stats4, utils, RBGL, XML, tools, gridExtra, Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, scales, flowViz
LinkingTo	Rcpp, BH (>= 1.62.0-1), RProtoBufLib, cytolib(>= 0.99.6)
Suggests	testthat, flowWorkspaceData, RSVGTipsDevice, knitr, ggcyto, parallel
SystemRequirements	xml2, GNU make, C++11
Enhances
URL
Depends On Me	flowStats, ggcyto, openCyto, QUALIFIER
Imports Me	CytoML, flowDensity, openCyto, QUALIFIER
Suggests Me	COMPASS, flowClust, flowCore
Build Report

Package Archives

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

Source Package	flowWorkspace_3.26.9.tar.gz
Windows Binary	flowWorkspace_3.26.9.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	flowWorkspace_3.26.9.tgz
Source Repository	git clone https://git.bioconductor.org/packages/flowWorkspace
Package Short Url	http://bioconductor.org/packages/flowWorkspace/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive