flowWorkspace

DOI: 10.18129/B9.bioc.flowWorkspace    

This package is for version 3.13 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: 3.13

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 <greg at ozette.ai>, Mike Jiang <mike at ozette.ai>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("flowWorkspace")

For older versions of R, please refer to the appropriate Bioconductor release.

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
PDF		Reference Manual
Text		NEWS
Text		INSTALL
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version	4.4.0
In Bioconductor since	BioC 2.9 (R-2.14) (10 years)
License	file LICENSE
Depends	R (>= 3.5.0)
Imports	Biobase, BiocGenerics, cytolib(>= 2.3.9), 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), DelayedArray, S4Vectors
LinkingTo	Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib(>= 2.3.7), Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1)
Suggests	testthat, flowWorkspaceData(>= 2.23.2), knitr, ggcyto, parallel, CytoML, openCyto
SystemRequirements	GNU make, C++11
Enhances
URL
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_4.4.0.tar.gz
Windows Binary	flowWorkspace_4.4.0.zip
macOS 10.13 (High Sierra)	flowWorkspace_4.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/flowWorkspace
Source Repository (Developer Access)	git clone [email protected]:packages/flowWorkspace
Package Short Url	https://bioconductor.org/packages/flowWorkspace/
Package Downloads Report	Download Stats