StaphVaccine_BCR

This study is for analyzing BCR data of staph vaccine (Cell Host and Microbe).

I. Script for generating Figure 4A

1. compareClonotypes.R: this script is used to compare clone types and generates figure 4a and EXCEL file (Clonotypes & Sample).
   • Input file: filtered_contig_annotations_SampleName.csv (generated from Cell Ranger "vdj" output).
     • Note: SampleName = "NT_IsdB","LAC_alum","LAC_lsdB"
   • Output files:
     • "compareClonotypes_aa.lsdB2.N=40.pdf" in the folder "results".
     • "compareClonotypes_aa.lsdB2.N=40.xlsx" in the folder "results".

II. Script for generating Figure 4B

2. clononetwork.py: generates figure 4b.
   • Input files:
     • filtered_contig_annotations_SampleName.csv (generated from Cell Ranger "vdj" output).
     • the filtered_feature_bc_matrix.h5 (generated from Cell Ranger "count" output).
   • Output file: "9_clonotype_network_20.png" in the folder "results".