suharoschi / flowfda

R package for analysing flow cytometry experiments with model based clustering, functional principal component analysis

flowFDA: Flow Cytometry Functional Data Analysis

Authors: Lieven Clement and Olivier Thas

flowFDA is an R package for analysing flow cytometry experiments with model based clustering, functional principal component analysis, functional discriminant analysis and to compare multivariate flow cytometry fingerprints accross treatments (De Roy, K., Clement, L., Thas, O., Wang, Y., and Boon, N. (2012). Flow cytometry for fast microbial community fingerprinting. Water Research, 46 (3), 907-919.). It will be released on R/Bioconductor in the future. The package is developed at Ghent University.

Installation

Install flowFDA from its GitHub repository. You first need to install the R/Bioconductor packages Biobase, BiocGenerics (>= 0.1.6), [flowCore] (http://bioconductor.org/packages/release/bioc/html/flowCore.html), flowViz, flowFP, graphics, grDevices, methods, stats, stats4, MASS, multcomp,mclust and devtools.

source("https://bioconductor.org/biocLite.R")
biocLite(c("flowCore", "flowViz", "flowFP", "MASS", "multcomp","mclust","devtools")

Then install flowFDAE using the install_github function in the devtools package. (With build_vignettes=TRUE, the vignettes will be built and installed.) You first need to install the flowFDADataExample package for this purpose

library(devtools)
install_github("lievenclement/flowFDAExampleData")
install_github("lievenclement/flowFDA", build_vignettes=TRUE)

###Vignettes Examples can be found in the vignettes

Regular analysis: vignette("flowFDA")

Analysis based on probability binning for backward compatibility with De Roy et al. (2012), Water Research, 46(3), 907-919: vignette("flowFDAProbabilityBinning")

Copyright

Copyright (C) 2016 Lieven Clement and Olivier Thas.

Licenses

The flowFDA package as a whole is distributed under GPL-3 (GNU General Public License version 3).

Contact

[email protected]