dli_reproducibility

Python scripts related to publication: Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy, Science Immunology. 2025.

Repo contains notebooks to recreate main paper figures. Links to data available at: https://www.azizilab.com/immunenetworks.html

Figure 1

• figure1.ipynb (1B, 1C, 1D, 1E, 1F)

Figure 2

• all_boxplots.ipynb (2A, 2C)
• DIISCO_CML_model.ipynb (2B)
• DIISCO_AML_model_run_3.ipynb (2D, 2E)
• DIISCO_AML_RL_interactions_run_1.ipynb (2F)
• DIISCO_AML_RL_interactions_run_3.ipynb (2F)

Figure 3

• codex_post_processing_niche_analysis.ipynb

Figure 4

Figure 5

• figure4_trajectory.ipynb (4A, 4B)
• aml_pd1_clean.R (4C, 4D, 4E)

Figure 6

• figure5_C0DEG_heatmap.ipynb (5A)

Figure 7

• AML_DLI_MERGE.ipynb (6A, 6B, 6C, 6D, 6E)
• TCR.ipynb (6F) (UPLOADED but need to clean up)

Methods developed by Azizi lab and used in paper:
DIISCO: Genome Research Publication, Method
Decipher:bioRxiv preprint, Method