scTCR

This repository contains the code used in our single cell sequencing paper: "T cell help shapes B cell tolerance"

Installation guide

Install dependencies listed below

Demo

Model data is included in the data directory.

Instructions

1. Download data and code directories
2. Set data as the working directory
3. Download gex and vdj data from GSE157649, available here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157649
4. Run each script in numerical order. These scripts will generate the figures presented in our manuscript.
   
   NB: Expected total run time is 3-5 days

System requirements and software

GLIPH v2
BLAST v2.12.0
NetMHCIIpan v4.1
cellranger v7.0.0

Python (v3.7.4) packages
AlphaFold v2.1.1
orfipy v0.0.4
GIANA v4.1
tcrdist3 v0.2.2
DeepTCR v2.1.0

R (v4.1.1) packages
harmony_0.1.0
Seurat_4.2.0
clusterProfiler_4.6.0
SPIA_2.50.0
qgraph_1.9.2
ggfortify_0.4.15
ggpubr_0.4.0.999
ggplot2_3.3.6
pheatmap_1.0.12