flowWorkspace

This is the released version of flowWorkspace; for the devel version, see flowWorkspace.

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

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DOI: 10.18129/B9.bioc.flowWorkspace

Bioconductor version: Release (3.22)

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 "4.5") 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")

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 4.22.0

In Bioconductor since BioC 2.9 (R-2.14) (14 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

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, 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_4.22.0.tar.gz

Windows Binary (x86_64) flowWorkspace_4.22.0.zip

macOS Binary (x86_64) flowWorkspace_4.22.0.tgz

macOS Binary (arm64) flowWorkspace_4.22.0.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/

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