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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 (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software
Version 4.15.5
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License AGPL-3.0-only
Depends R (>= 3.5.0)
Imports Biobase, BiocGenerics, 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++11
URL
See More
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 CytoML, flowStats, ImmuneSpaceR, openCyto, PeacoQC
Suggests Me CATALYST, COMPASS, flowClust, flowCore, FlowSOM
Links To Me CytoML
Build Report Build Report

Package Archives

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

Source Package flowWorkspace_4.15.5.tar.gz
Windows Binary flowWorkspace_4.15.5.zip
macOS Binary (x86_64) flowWorkspace_4.15.5.tgz
macOS Binary (arm64) flowWorkspace_4.15.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/flowWorkspace
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/flowWorkspace
Bioc Package Browser https://code.bioconductor.org/browse/flowWorkspace/
Package Short Url https://bioconductor.org/packages/flowWorkspace/
Package Downloads Report Download Stats