Link to bioarXiv preprint: https://www.biorxiv.org/content/10.1101/2024.02.09.579677v1
Repo contains notebooks to recreate paper figures. Count data and CITE data deposited at GEO upon publication. Other data used in notebooks deposited here upon publication.
- figure1.ipynb (1B, 1C, 1D, 1E, 1F)
- 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)
- codex_post_processing_niche_analysis.ipynb
- figure4_trajectory.ipynb (4A, 4B)
- aml_pd1_clean.R (4C, 4D, 4E)
- figure5_C0DEG_heatmap.ipynb (5A)
- AML_DLI_MERGE.ipynb (6A, 6B, 6C, 6D, 6E)
- TCR.ipynb (6F) (UPLOADED but need to clean up)
- numbat_preprocess.ipynb, numbat_preprocess.R, numbat_plot_heatmap.R (S1I)
- figure_S1.ipynb (S1E, S1F, S1G, S1H, S1J, S1K, S1L, S1O)
- cite_seq_normalization.ipynb (S1M, S1N, S1P)
- all_boxplots.ipynb
- DIISCO_CML_model.ipynb (S3B, S3C, S3D)
- DIISCO_CML_RL_interactions.ipynb (S3E)
- DIISCO_AML_model_run_3.ipynb (S4A)
- DIISCO_AML_model_run_1.ipynb (S4B)
- AML_DLI_MERGE.ipynb (S4C)
- figure4_trajectory.ipynb (S4F, S4G, S4H, S4I)
- codex_post_processing_niche_analysis.ipynb (S4E)
- aml_pd1_clean.R
- km_test_20231002.R
- AML_DLI_MERGE.ipynb (6A, 6B, 6C, 6D, 6E)
- TCR.ipynb
- all_boxplots.ipynb