--- a
+++ b/Cydar/README.md
@@ -0,0 +1,8 @@
+# Cydar Analysis
+
+This folder contains scripts that were used to perform the Cydar analysis on the protein expression data.
+The scripts are in order of how they are run to process the data and take the background corrected ADT expression SCE object as input.
+
+- 01_fastMNN.R performs batch correction on the background corrected protein counts
+- 02_CreateHyper.R assigns cells into hyperspheres
+- 03_Cydar_Figure.Rmd then test for differential abundance of cells in each sphere and produces the plots from the manuscript