guokai8 / Cd8_T_cell

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 paramaters by using "cellranger count". Details for alignment will be found in the "web_summary.html" in the 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 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