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("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 | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
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 |
See More
| 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 |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | flowWorkspace_4.2.0.tar.gz |
| Windows Binary | flowWorkspace_4.2.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | flowWorkspace_4.2.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |