Code for the analysis of samples used in the manuscript "Immune profiling-based targeting of pathogenic T cells with ustekinumab in ANCA-associated glomerulonephritis"

Instructions for single-cell analysis

System requirements and installation

We ran the code in an Ubuntu 20.04 environment. To setup the single-cell analysis Python environment, please run the following commands:

conda env create -f envs/sc-env.yml
conda activate sc-env

Data preparation

Place the cellranger-aligned data in the folder data. For the correct version please refer to the methods section of the manuscript.

Analysis workflow

The analysis workflow for the single-cell data (CITEseq and scRNAseq) is detailed in the folder notebooks\single-cell. We further split the code for each cohort, namely the exploratory and the ustekinumab treatment cohort. The corresponding code is available in the folders notebooks\single-cell\exploratory_cohort and notebooks\single-cell\ustekinumab_cohort, respectively.

Instructions for Visium analysis

Data preparation

1. Place the cellranger- and spaceranger-aligned data in folder data. For the versions used in the manuscript, please refer to the methods section of the manuscript.
2. Place the TIF files corresponding to each spatial sample in the folder tif_processed

The folders annotations_visium* contain expert-annotations of the Visium samples

Analysis workflow

Guided code for required to reproduce the results is available in the folder notebooks. The second step of the processing is too big to push to GitHub, this can be downloaded from 02_cluster.ipynb

If you encounter any problem, please open an issue.