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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("flowFlowJo")
In most cases, you don't need to download the package archive at all.
flowFlowJo
Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.
Bioconductor version: 3.0
FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.
Author: John J. Gosink <gosinkj at amgen.com>
Maintainer: John J. Gosink <gosinkj at amgen.com>
Citation (from within R,
enter citation("flowFlowJo")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("flowFlowJo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("flowFlowJo")
| R Script | Basic Functions for working with FlowJo | |
| Reference Manual |
Details
| biocViews | FlowCytometry, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) |
| License | GPL (>=3) |
| Depends | R (>= 2.5.0), MASS |
| Imports | flowCore, XML (>= 1.96), methods, Biobase |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | flowFlowJo_1.24.0.tar.gz |
| Windows Binary | flowFlowJo_1.24.0.zip |
| Mac OS X 10.6 (Snow Leopard) | flowFlowJo_1.24.0.tgz |
| Mac OS X 10.9 (Mavericks) | flowFlowJo_1.24.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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