PeriNeuroImmuneMap

Multi-Scale Spatial Transcriptomics Framework for Perineural Neuroimmune Coupling

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Overview

PeriNeuroImmuneMap is a research-grade computational pipeline for characterizing perineural neuroimmune coupling using spatial transcriptomics and integrative downstream analyses.

The repository is organized as a modular, notebook-first pipeline with reproducible execution order, clear I/O conventions, and publication-oriented outputs.

Repository: https://github.com/Sjtu-Fuxilab/PeriNeuroImmuneMap

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What this repository contains

• 01 — Data Processing & QC: input harmonization, QC, preprocessing
• 02 — Nerve Injury Signature: derivation, validation, benchmarking
• 03 — Immune Landscape: spatial immune programs & external validation
• 04 — Communication Networks: nerve–immune–tumor interactions (LR/network analysis)
• 05 — Circadian/Symptom Analysis: cohort-scale analysis and translational stratification

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Repository structure

PeriNeuroImmuneMap/
├── notebooks/
│   ├── 01_data_processing_qc.ipynb
│   ├── 02_nerve_signature_derivation.ipynb
│   ├── 03_immune_landscape_analysis.ipynb
│   ├── 04_communication_networks.ipynb
│   └── 05_circadian_symptom_analysis.ipynb
├── requirements.txt
├── environment.yml
├── LICENSE
└── README.md

Note: Large datasets and generated outputs should not be committed. Keep the repo lean and reproducible via .gitignore.

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Installation

Option A — Conda (recommended)

git clone https://github.com/Sjtu-Fuxilab/PeriNeuroImmuneMap.git
cd PeriNeuroImmuneMap

conda env create -f environment.yml
conda activate perineuroimmuemap

Option B — Pip

pip install -r requirements.txt

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Usage

Launch Jupyter and run notebooks in order:

jupyter notebook

Execution order:

1. notebooks/01_data_processing_qc.ipynb
2. notebooks/02_nerve_signature_derivation.ipynb
3. notebooks/03_immune_landscape_analysis.ipynb
4. notebooks/04_communication_networks.ipynb
5. notebooks/05_circadian_symptom_analysis.ipynb

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Reproducibility expectations

• Deterministic seeds where applicable
• Explicit software versions (environment files)
• Separation of data, code, and outputs
• Notebook headers defining Inputs / Outputs / Runtime

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Citation

If you use this pipeline, please cite:

@article{zafar2026perineural,
  title     = {Perineural Neuroimmune Coupling Disrupts Circadian Regulation and Drives Behavioral Symptom Burden in Cancer},
  author    = {Zafar, Sanwal Ahmad and Qin, Wei and others},
  journal   = {Neuroimmunomodulation},
  year      = {2026},
  publisher = {Karger}
}

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Correspondence

Assoc. Prof. Wei Qin Associate Dean, Institute of Industrial Engineering and Management Shanghai Jiao Tong University, China
Email: wqin@sjtu.edu.cn