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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")
In most cases, you don't need to download the package archive at all.
flowWorkspace
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see flowWorkspace.
Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
Bioconductor version: 3.2
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>
Citation (from within R,
enter citation("flowWorkspace")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("flowWorkspace")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("flowWorkspace")
| R Script | Importing flowJo Workspaces into R | |
| HTML | How to merge GatingSets | |
| HTML | How to parse gatingML into a GatingSet | |
| HTML | How to plot gated data | |
| Reference Manual | ||
| Text | NEWS | |
| Text | INSTALL |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, Preprocessing, Software |
| Version | 3.16.16 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.16.0), flowCore(>= 1.36.4), flowViz(>= 1.29.27), ncdfFlow(>= 2.16.1), gridExtra |
| Imports | Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, XML, tools, gridExtra, Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, flowUtils, jsonlite |
| LinkingTo | Rcpp, BH (>= 1.60.0-1) |
| Suggests | testthat, flowWorkspaceData, RSVGTipsDevice, knitr |
| SystemRequirements | xml2, GNU make |
| Enhances | |
| URL | |
| Depends On Me | flowStats, openCyto, QUALIFIER |
| Imports Me | openCyto, QUALIFIER |
| Suggests Me | COMPASS, flowCore |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | flowWorkspace_3.16.16.tar.gz |
| Windows Binary | flowWorkspace_3.16.16.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | flowWorkspace_3.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | flowWorkspace_3.16.16.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/flowWorkspace/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/flowWorkspace/ |
| Package Downloads Report | Download Stats |
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