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Bioconductor - flowWorkspace (development version)

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 (3.22)

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")

# 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")
Details biocViews DataImport, DataRepresentation, FlowCytometry, ImmunoOncology, Preprocessing, Software Version 4.21.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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, 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.

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