Dock8 scRNAseq Analysis Code — Chen et al.

This repository contains all the code used in the analysis for the manuscript:

"DOCK8-STAT3 Complexes Regulate Mucosal Immune Tolerance"
Chen et al.

• Manuscript: [Link] (DOI: [..])
• Contact: Qian Chen — qianchen8828@gmail.com / Talal Chatila - talal.chatila@childrens.harvard.edu

---

Overview

This repository collects the scripts for processing and analyzing single-cell RNA sequencing (scRNAseq) data as described in the manuscript.
Preliminary analyses were performed using Cellranger (10x Genomics). The analysis workflow was performed using Seurat v5, with additional supporting R packages.

---

Analysis Workflow

1. Quality Control and Processing (Seurat)

   • See: script/1_QC_and_processing.R
   • Import filtered matrices from CellRanger, quality control, filtering, normalization, integration, and clustering.

2. Imputation and Differential Gene Expression (Seurat)

   • See: script/2_Imputation_DE_genes.R
   • Imputation and Identification of differentially expressed genes.

3. Visualization and Figure Generation (Seurat)

   • See: script/3_Plots.R
   • Generation of all figures and plots included in the manuscript.

---

Data Availability

• Raw sequencing data: Available at GEO/SRA: GSE303265
• Processed Seurat object: Available on Zenodo (DOI: ) Processed data will be available upon publication

---

Requirements

All R package dependencies and the R version used for this analysis are specified in the renv.lock file included in this repository.

To recreate the exact software environment, install the renv package in R and run:

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

This will install the correct R packages and versions as used for the original analysis.

Note:
The analysis was performed using R version 4.4.1
For details about all package versions, please refer to the renv.lock file.

---

Usage

1. Clone the repository:

   git clone https://github.com/tuo-utente/nome-repo.git
   cd nome-repo

2. Follow the scripts in the order described above.
   Please refer to comments within each script for details on requirements and parameters.

Note:
For Cellranger usage, refer to the 10x Genomics documentation.

---

Issues & Contact

If you encounter any problems or have questions, please open an issue in this repository or contact Dr. Qian Chen at qianchen8828@gmail.com and Dr. Olga Lanzetta at olga.lanzetta@edu.unige.it

---