flowWorkspace

DOI: 10.18129/B9.bioc.flowWorkspace    

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

Bioconductor version: Release (3.15)

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>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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 4.8.0
In Bioconductor since BioC 2.9 (R-2.14) (11 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, rmarkdown, 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_4.8.0.tar.gz
Windows Binary flowWorkspace_4.8.0.zip
macOS Binary (x86_64) flowWorkspace_4.8.0.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 https://bioconductor.org/packages/flowWorkspace/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: