Spatial Analysis of T Cell Clonality in Autoimmune Kidney Disease Using TRV Probes

This repository contains code and analysis notebooks for the manuscript Spatial Analysis of T Cell Clonality in Autoimmune Kidney Disease Using TRV Probes.

Installation (Conda + Poetry)

Prerequisites: Conda (Mambaforge/Miniconda/Anaconda) and Git installed.

1. Create and activate a Python 3.10 environment

conda create -n spatialtcr python=3.10 -y
conda activate spatialtcr

2. Install Poetry inside the active Conda environment (if not present)

conda install -c conda-forge poetry -y
# Make Poetry use the currently active Conda Python (recommended)
poetry config virtualenvs.prefer-active-python true

3. Download code and install dependencies

git clone https://github.com/imsb-uke/spatial-tcr.git
cd spatial-tcr
poetry install

Usage

The notebooks folder contains separate analysis folders:

• The XeniumTCR-analysis folder contains the notebooks for the spatial analysis of the Xenium TCR data.
• The TCRseq-analysis folder contains code to analyze the single-cell TCRseq data.