flowWorkspace

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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

Bioconductor version: Development (3.24)

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.com>, Mike Jiang <mike at ozette.com>

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

Greg Finak, Mike Jiang. flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets. doi:10.18129/B9.bioc.flowWorkspace, R package version 4.25.1, https://bioconductor.org/packages/flowWorkspace.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

flowWorkspace Introduction: A Package to store and maninpulate gated flow data	HTML	R Script
How to merge GatingSets	HTML	R Script
Reference Manual	PDF
NEWS	Text
INSTALL	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version	4.25.1
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	AGPL-3.0-only
Depends	R (>= 3.5.0)
Imports	Biobase, BiocGenerics (>= 0.59.5), cytolib (>= 2.13.1), XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, scales (>= 1.3.0), matrixStats, RProtoBufLib, flowCore (>= 2.1.1), ncdfFlow (>= 2.25.4), DelayedArray, S4Vectors
System Requirements	GNU make, C++17
URL

Suggests	testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto
Linking To	cpp11, BH (>= 1.62.0-1), RProtoBufLib (>= 1.99.4), cytolib (>= 2.3.7), Rhdf5lib
Enhances
Depends On Me	flowGate, ggcyto, highthroughputassays
Imports Me	CyFj11, CytoML, flowStats, openCyto, PeacoQC, polyICSFlow, staRgate
Suggests Me	CATALYST, flowClust, flowCore, FlowSOM
Links To Me	CytoML
Build Report	Build Report, r-universe

Package Archives

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

Source Package	flowWorkspace_4.25.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	flowWorkspace_4.25.1.tgz
macOS Binary (sonoma-arm64)	flowWorkspace_4.25.1.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