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.spilloverExamples
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.