diff --git a/.gitignore b/.gitignore
index 33ffe52..011d802 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ data/clinical-data
 app/*backup
 backup/
 scripts/update-namemaps.py
+prep_sc_data.R
diff --git a/app/app.R b/app/app.R
index 0400602..dce09ee 100644
--- a/app/app.R
+++ b/app/app.R
@@ -13,7 +13,6 @@ library(shinyWidgets)
 library(shinycssloaders)
 library(shinydashboard)
 
-
 source("utils.R")
 options(shiny.usecairo = FALSE)
 
@@ -30,10 +29,6 @@ imdims.list <- readRDS("data/imdims.list")
 dims.list <- readRDS("data/dims.list")
 data.list <- readRDS("data/data.list")
 
-sc.list <- readRDS("data/cs.list")
-scs <- Reduce(intersect, lapply(sc.list,
-                                colnames))
-
 c(t1.list,
   t2.list,
   t3.list) %<-% lapply(1:3,
@@ -54,7 +49,7 @@ c(t1.cells,
 #### UI ####
 
 ui <- dashboardPage(
-  
+
   header = dashboardHeader(title = "HER2+ BC"),
 
   sidebar = dashboardSidebar(
diff --git a/app/data/cs.list b/app/data/cs.list
deleted file mode 100644
index 4a692e7..0000000
Binary files a/app/data/cs.list and /dev/null differ
diff --git a/app/data/t1.list b/app/data/t1.list
index 217fe26..3fde4b2 100644
Binary files a/app/data/t1.list and b/app/data/t1.list differ
diff --git a/app/data/t2.list b/app/data/t2.list
index 23ea8fa..7c711ec 100644
Binary files a/app/data/t2.list and b/app/data/t2.list differ
diff --git a/app/data/t3.list b/app/data/t3.list
index 1b80a30..8f8c2de 100644
Binary files a/app/data/t3.list and b/app/data/t3.list differ
diff --git a/app/utils.R b/app/utils.R
index 19e29f5..3065118 100644
--- a/app/utils.R
+++ b/app/utils.R
@@ -4,7 +4,7 @@ require(RColorBrewer)
 # FUNCTIONS -----------
 
 make_empty_theme <- function(){
-  theme_empty <- theme_bw() 
+  theme_empty <- theme_bw()
   theme_empty$line <- element_blank()
   theme_empty$rect <- element_blank()
   theme_empty$strip.text <- element_blank()
@@ -23,7 +23,7 @@ make_empty_theme <- function(){
   theme_empty$legend.title <- element_text(colour = "white")
   theme_empty$strip.background <- element_rect(fill="black")
   theme_empty$legend.key.size <- unit(10,"mm")
-  theme_empty$legend.margin <- margin(10,50,10,50) 
+  theme_empty$legend.margin <- margin(10,50,10,50)
 
   return(theme_empty)