This repository contains the scripts and notebooks to reproduce the analyses performed in the Harreman manuscript:
Metabolic zonation and characterization of tissue slices with spatial transcriptomics https://doi.org/10.1101/2025.11.11.687271
The repository is structured as follows:
- Harreman_Hotspot_comparison: This folder contains all the scripts and notebooks needed to reproduce Figure S1.
- Parametric_vs_non_parametric_tests: This folder contains the notebook needed to reproduce Figure S2.
- Slide_seq_lung: This folder contains the scripts and notebooks needed to process the Slide-seq human lung dataset as well as to reproduce Figures 2, 3, S3, S4, S5, and S6.
- Visim_colon: This folder contains the scripts and notebooks needed to process the 10x Visium mouse colon dataset as well as to reproduce Figures 4, 5, S7, S8, S9, and S10.