A density-based automated gating pipeline for flow cytometry data to characterize the lineage, differentiation, and functional states of T-cells

This GitHub stores the {staRgate} R package.

Installation

The {staRgate} package relies on a few Biocondcutor R packages. Before installing {staRgate}, first setup Bioconductor and install all packages.

{flowCore} and {flowWorkspace} are dependencies for the {staRgate} package
{openCyto}, {flowAI}, {ggcyto} are not required to run the functions of {staRgate} but are used in the full gating pipeline as shown in the Tutorial

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

To install staRgate (currently install from GitHub):

devtools::install_github("leejasme/staRgate")

Tutorial