Code of single cell analysis of SLE samples

This repo keeps the reproducible analysis pipeline of our manuscript "Global immune repertoire profiling suggests multifaceted unresolved dysregulation upon systemic lupus erythematosus immunosuppressant therapy".

Setup environment

R env

We use R-4.2.1, and record the all used R packages and their version in renv.lock file. To reproduce our environment, just run

install.packages("renv")
renv::restore()

Python env

We use conda to manage Python environment. To reproduce the environment, run

conda env create --name <ENV_NAME> --file=environments.yml

Java (optional)

If you want to run VDJtools, please install Java following https://www.java.com/.

Code structure

The code is organized as follows:

.
│── Figure/            # dir of the scripts for reproducing figures in the manuscript
│── data/              # dir of the input data
│── atlas/             # dir of the scripts for building the single cell SLE atlas
│── output_file/       # dir of the key outputs of the analysis pipeline
├── scripts/           # dir of the scripts for RNA analysis
│── vdj/               # dir of the scripts for BCR analysis
│── tcr_vdj/           # dir of the scripts for TCR analysis
│── renv.lock          # file keeps R packages and their version
├── environments.yml   # file keeps conda environment

And there will be detailed instructions in each folder.

Data

Single cell RNA matrix and VDJ data will be available upon publication.

Reproduce the analysis

RNA

We mainly use R package Seurat to analyze single cell RNA data, and analysis pipeline is in directory scripts/seurat. Other specific analysis is also in scripts/, such as scripts/monocle2, scripts/CellChat and scripts/scvelo.

TCR and BCR

We use R package immcatation, VDJtools and scRepertoire to analyze the single cell TCR/BCR data. The analysis pipeline is in tcr_vdj/ and vdj respectively.

Reproduce plots in the manuscript

Run Figure/Figures_plot.R to reproduce main figures in manuscript. Input data needs to be requested from the authors. (we can not put it online due to the privacy of the patients)

Publication

Our manuscript is under review.

Contact

If you have any questions, please contact Chen-Rui Xia ([email protected]) or open an issue on GitHub.