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dli_reproducibility

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.

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

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

Figure 5

  • figure5_C0DEG_heatmap.ipynb (5A)

Figure 6

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

Figure S1

  • 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)

Figure S2

  • all_boxplots.ipynb

Figure S3

  • DIISCO_CML_model.ipynb (S3B, S3C, S3D)
  • DIISCO_CML_RL_interactions.ipynb (S3E)

Figure S4

  • 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)

Figure S5

  • aml_pd1_clean.R
  • km_test_20231002.R

Figure S6

  • AML_DLI_MERGE.ipynb (6A, 6B, 6C, 6D, 6E)
  • TCR.ipynb
  • all_boxplots.ipynb

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Notebooks to recreate paper figures

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