autospill

The autospill package implements the AutoSpill algorithm for calculating spillover coefficients, used to compensate or unmix flow cytometry data.

For more details, please see:
Roca et al: AutoSpill: A method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data. bioRxiv 2020.06.29.177196; doi:10.1101/2020.06.29.177196 (2020).

Installation

To install autospill from this GitHub repository, use the function install_github in the devtools package.

library( devtools )

install_github( "carlosproca/autospill" )

Help

You can use the standard help in R.

library( autospill )

? get.marker.spillover
? refine.spillover

Examples

Please see the example scripts in the batch folder after installing the package.

The scripts calculate_compensation_paper.r and calculate_compensation_paper.sh can be used to reproduce the results of AutoSpill for single-color controls appearing in the paper above. For this, you will need to download the datasets (FCS files and auxiliary fcs_control.csv files) from FlowRepository: MM1 dataset, HS1 & HS2 datasets, and Be1 dataset.

The scripts calculate_compensation_website.r and calculate_compensation_website.sh can be used to reproduce the results obtained at the AutoSpill website.