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README.md

@@ -36,7 +36,7 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
 ## Libraries 
 <details><summary>Code</summary> 
 <p>
-```{r libraries, include=FALSE}
+```r
 library(reticulate)
 use_python("C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe", required = TRUE)
 options(future.globals.maxSize= 2122317824)
@@ -63,7 +63,7 @@ set.seed(123)
 ## Setting Up
 <details><summary>Code</summary> 
 <p>
-```{r setup}
+```r
 # ================================ SETTING UP ======================================== #
 tool="seurat"
 project ="Michi_Data"
@@ -105,7 +105,7 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
 
 <details><summary>Code</summary> 
 <p>
-```{r readfiles}
+```r 
 # ======== Perform an integrated analysis ====
 NewDir <- paste0(Sys.Date(),"_",tool,"_elbow_",elbow,"_Mito-",remove_mt,"_Ribo-",remove_ribsomal,"_SCT-",SCT,"_criteria_pass-",criteria_pass)
 dir.create(NewDir)