The project new URL is now https://gitbio.ens-lyon.fr/lmodolo/yellow_fever

Divergent Patterns of Clonal CD8+ T Cell Differentiation Give Rise to Distinct Lineages of Memory T cells Following Human Viral Infections

This repository contains the script and package used for the analysis of the paper.

Installation

To get the code and install the nessessary R package you need to run the following commands:

git clone git@github.com:LBMC/yellow_fever.git
cd yellow_fever

If you are on Ubuntu you will also need the following dependency for R:

sudo add-apt-repository "deb https://stat.ethz.ch/CRAN/bin/linux/ubuntu xenial/"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update -y
sudo apt-get install -y r-base r-base-dev libcurl4-gnutls-dev libxml2-dev libssl-dev

Then go in the repository folder and install the following packages in R:

source("src/00_functions.R")

Analysis

All the scripts used for the analyses can be found in the src/ folder.

The scripts are numbered from 0_1, 01 to 05 in execution order with 01_QC.R the first script for scRNASeq data analysis (the 0_1, is independent from the rest of the pipeline). The scirpt numbered from 1 to 12 correspond to an old version of the pipeline not using SingleCellExperiment object.