Welcome to polyICSFlow

Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data.

polyICSFlow systematically identifies all cytokine combinations detected in an Intracellular Cytokine Staining (ICS) Flow Cytometry assay and quantifies polyfunctional antigen-specific responses to single or multiple antigens. The package requires as input preprocessed data in the form of a gatingHierarchy or a gatingSet gated on the cytokines of interest.

Citation

If you use this package, please cite:

citation("polyICSFlow")

Installation

You can install the development version of polyICSFlow from GitHub with:

# install.packages("pak")
pak::pak("SoegaardLab/polyICSFlow")

Or from Bioconductor

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("polyICSFlow")

How it works

polyICSFlow is designed as a sequential workflow of three functions, where the output of each function serves as the input to the next:

  1. getMarkerPositivity() generates a cell-by-marker positivity matrix
  2. assignMarkerCombinations() assigns marker combinations to each cell
  3. calcPolyfunctionality() computes frequencies and background-subtracted responses

For more in-depth walk through of the workflow, check out function documentation and the vignettes:

browseVignettes("polyICSFlow")