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, S6, and S7.
-
Visium_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, S8, S9, S10, and S11.
-
Visium_RCC: This folder contains the scripts and notebooks needed to process the 10x Visium human ccRCC dataset as well as to reproduce Figure 6.
-
Method_benchmarking: This folder contains the notebooks needed to reproduce Figure S12, which benchmarks Harreman against scCellFie across five complementary axes.
-
Parameter_benchmarking: This folder contains the notebooks needed to reproduce Figures S13 and S15, which assess the robustness of Harreman to parameter choices and metabolite binarization strategies, respectively.
-
Transporter_promiscuity_analysis: This folder contains the notebook needed to reproduce Figure S14, which assesses the impact of transporter annotation coverage and promiscuity on Harreman metabolite-level scores.