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FAUST

Full Annotation Using Shape-constrained Trees

The FAUST package implements the FAUST method described in A new data-driven cell population discovery and annotation method for single-cell data, FAUST, reveals correlates of clinical response to cancer immunotherapy.

The FAUST package requires Rcpp and devtools, and that a C++11 compiler is available.

Installation

Currently faust must be installed from its source. It depends on the scamp package.

The most recent version can be installed from github using devtools in R. A quick installation (without vignettes) can be performed by:

tryCatch(installed.packages()["BiocManager","Version"],
     error = function(e){
            install.packages("BiocManager")
         })	
library(BiocManager)
BiocManager::install("Biobase", update = FALSE)
BiocManager::install("flowCore", update = FALSE)
BiocManager::install("flowWorkspace", update = FALSE)
BiocManager::install("flowWorkspaceData", update = FALSE)
BiocManager::install("cytolib", update = FALSE)
BiocManager::install("CytoML", update = FALSE)

library(devtools)
devtools::install_github("RGLab/scamp")
devtools::install_github("RGLab/FAUST")

To build the vignettes during installation, instead run:

tryCatch(installed.packages()["knitr","Version"],
     error = function(e){
            install.packages("knitr")
         })	
tryCatch(installed.packages()["rmarkdown","Version"],
     error = function(e){
            install.packages("rmarkdown")
         })
tryCatch(installed.packages()["ggdendro","Version"],
     error = function(e){
            install.packages("ggdendro")
         })
devtools::install_github("RGLab/FAUST", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

This takes longer since the vignettes must be built from source.

After loading FAUST, type vignette('faustIntro') to read a vignette discussing how to use the FAUST function in R.

Citation

If you end up using FAUST to analyze cytometry datasets, please consider citing A new data-driven cell population discovery and annotation method for single-cell data, FAUST, reveals correlates of clinical response to cancer immunotherapy.

faust's People

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