Update README.md

README.md

@@ -6,9 +6,10 @@ Principal Investigator: William Schief, PhD
 Institution: Scripps Research  
 Email: [email protected]   
 
-DATA OVERVIEW
+# DATA OVERVIEW
 
 The "data" folder contains 5 csv files as follows:    
+
 1. cvd725_ics_2022DEC27.csv:     
 	This file contains data to plot the background-adjusted frequencies of cytokine-positive eOD-GT8 and LumSyn-specific CD4 (Figure 1B) and CD8 (Figure 1D) T cells at week 10.    
 	     
@@ -18,6 +19,7 @@ The "data" folder contains 5 csv files as follows:
 
 
 2. cvd725_Tfh_ics_2022DEC23.csv:      
+
 	This file contains data to plot the frequencies of vaccine-specific cTfh-like cells measured in the PBMC at week 10 (Figure 1C) as the background-adjusted percent of IL-2+ or CD40L+ CXCR5+ CD4+ T cells out of total circulating CD4 T cells by stimulation.     
 
 	Number of variables: 12      
@@ -26,6 +28,7 @@ The "data" folder contains 5 csv files as follows:
 
 
 3. cvd725_cluster_ics_2022DEC23.csv:     
+
 	This file contains data to generate results from the K-means clustering analysis (Figure 2) conducted on CD4 T cells that were positive	for at least 2 cytokines or activation markers in the eOD-GT8, LumSyn, negative control, and CMV stimulations by ICS assay.     
 	        
 	Number of variables: 23     
@@ -34,6 +37,7 @@ The "data" folder contains 5 csv files as follows:
 
 
 4. cvd725_epitope_mapping_ics_2022DEC28.csv:       
+
 	This file contains data to map the immunodominant T cell responses to eOD-GT8 and LumSyn (Figure 3).      
 	      
 	Number of variables: 48      
@@ -42,6 +46,7 @@ The "data" folder contains 5 csv files as follows:
 
 
 5. cvd725_association_TandBcell_2022DEC28.csv:      
+
 	This file contains data needed to associate the frequencies of T and B cell responses within and between peripheral and lymph node compartments (Figure 4).       
 
 	Number of variables: 14          
@@ -51,18 +56,21 @@ The "data" folder contains 5 csv files as follows:
 
 
 
-
-CODE OVERVIEW 
+# CODE OVERVIEW 
 
 NOTE: The current version of the code (which was used for the study) does not function on de-identified data.
 
 The "code" folder contains 3 .R files as follows:
+
 1. Tcell-figures.R:    
+
   This code reads in cvd725_ics_2022DEC27.csv, cvd725_tfh_ics_2022DEC23.csv, and cvd725_association_TandBcell_2022DEC28.csv and plots Figures 1B, 1C, 1D and 4 in the T-cell manuscript.
 
 2. epitope_mapping_report.R:   
-	This code reads in cvd725_epitope_mapping_ics_2022DEC28.csv to map the immunodominant T cell responses to eOD-GT8 and LumSyn (Figure 3).
+
+  This code reads in cvd725_epitope_mapping_ics_2022DEC28.csv to map the immunodominant T cell responses to eOD-GT8 and LumSyn (Figure 3).
 
 3. UMAP-figures.R:     
+
   This code reads in cvd725_cluster_ics_2022DEC27.csv and generates results from the K-means clustering analysis (Figure 2).