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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
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Infrastructure for representing and interacting with the gated cytometry
Bioconductor version: Release (3.5)
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
| HTML | R Script | How to merge GatingSets |
| HTML | R Script | How to plot gated data |
| Reference Manual | ||
| Text | NEWS | |
| Text | INSTALL |
Details
| biocViews | DataImport, DataRepresentation, FlowCytometry, Preprocessing, Software |
| Version | 3.24.4 |
| In Bioconductor since | BioC 2.9 (R-2.14) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.16.0), flowCore(>= 1.39.9), ncdfFlow(>= 2.19.5) |
| Imports | Biobase, BiocGenerics, graph, graphics, lattice, methods, stats, stats4, utils, RBGL, XML, tools, gridExtra, Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, scales, flowViz |
| LinkingTo | Rcpp, BH (>= 1.62.0-1) |
| Suggests | testthat, flowWorkspaceData, RSVGTipsDevice, knitr, ggcyto, parallel |
| SystemRequirements | xml2, GNU make, C++11 |
| Enhances | |
| URL | |
| Depends On Me | flowStats, ggcyto, openCyto, QUALIFIER |
| Imports Me | CytoML, openCyto, QUALIFIER |
| Suggests Me | COMPASS, flowClust, flowCore |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | flowWorkspace_3.24.4.tar.gz |
| Windows Binary | flowWorkspace_3.24.4.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | flowWorkspace_3.24.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/flowWorkspace |
| Package Short Url | http://bioconductor.org/packages/flowWorkspace/ |
| Package Downloads Report | Download Stats |
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