The chemokine receptor CXCR3 promotes CD8 T cell dependent lung pathology during influenza pathogenesis

# The chemokine receptor CXCR3 promotes CD8 T cell-dependent lung pathology during influenza pathogenesis

### Description

Data were collected after mapping all fastq files to the mm10 genome with the cellranger v5.0 software with default parameters by using "cellranger count". Details for alignment will be found in the "web_summary.html" in each data file

### Required packages:

Seurat v3, CellChat, tidyverse, richR, scGSVA, VennDetail, SCENIC(v1.2.2), ggrepel

install.packages(c('Seurat','tidyverse'))

BicManager::install(c("CellChat","VennDetail","SCENIC"))

devtools::install_github('guokai8/richR')

devtools::install_github('guokai8/scGSVA')

### Download data

git clone https://github.com/guokai8/Cd8_T_cell/

cd Cd8_T_cell

Then load data into R 4.0.2 and do the analysis by following the below steps

#### Step1 (Fig.2, Fig.S2, Fig.S3, Data S1-S9)

run the Tcell_clustering.R for clustering, Cell annotation, Differential expressed analysis, and GSEA.

#### Step2 (Fig.4, Fig.S3)

run the tcell_cell.r for the cell-cell communication analysis

#### Step3 (Fig.4)

run the tcell_scenic.r for the TF network analysis