flowWorkspace

DOI: 10.18129/B9.bioc.flowWorkspace    

This is the development version of flowWorkspace; for the stable release version, see flowWorkspace.

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

Bioconductor version: Development (3.8)

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:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("flowWorkspace", version = "devel")

Documentation

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

browseVignettes("flowWorkspace")

 

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 3.29.9
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License Artistic-2.0
Depends R (>= 2.16.0), flowCore(>= 1.45.14), ncdfFlow(>= 2.25.4)
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, matrixStats
LinkingTo Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.2)
Suggests testthat, flowWorkspaceData, 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
Links To Me
Build Report  

Package Archives

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

Source Package flowWorkspace_3.29.9.tar.gz
Windows Binary flowWorkspace_3.29.9.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) flowWorkspace_3.29.9.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 http://bioconductor.org/packages/flowWorkspace/
Package Downloads Report Download Stats

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