flowWorkspace

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see flowWorkspace.

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

Bioconductor version: 3.12

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 <gfinak at fhcrc.org>,Mike Jiang <wjiang2 at fhcrc.org>,Jake Wagner <jpwagner at fhcrc.org>

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

Installation

To install this package, start R (version "4.0") 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 4.2.0

In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)

License file LICENSE

Depends R (>= 3.5.0)

Imports Biobase, BiocGenerics, cytolib(>= 2.1.20), 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)

System Requirements GNU make, C++11

URL

Suggests testthat, flowWorkspaceData(>= 2.23.2), knitr, ggcyto, parallel, CytoML, openCyto

Linking To Rcpp, BH (>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib(>= 2.1.15), Rhdf5lib, RcppArmadillo, RcppParallel (>= 4.4.2-1)

Enhances

Depends On Me ggcyto, highthroughputassays

Imports Me CytoML, flowDensity, FlowSOM, flowStats, ImmuneSpaceR, openCyto, PeacoQC

Suggests Me CATALYST, COMPASS, flowClust, flowCore

Links To Me CytoML

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