Reproduce Decipher paper figures

This repository contains the notebooks used to produce the figures of the Decipher paper. The Decipher code used in these notebook is available at:

1. https://github.com/azizilab/decipher at commit: 63b7d25c44bf1bbfa65ca7865e41b6c9b0abcf07.
2. https://github.com/azizilab/decipher/releases/tag/reproducibility at tag: reproducibility.
3. included in this repo in the decipher_code directory.

For using Decipher, we recommend using the latest version at https://github.com/azizilab/decipher. It is more documented and has more features.

Figure 1

• simulated_data.ipynb

Figure 2

• simulation/
  • Run simulation.py, then generate_figures.py

Figure 3

• Figure_3_PDAC.ipynb
• pdac_scvi.ipynb

Figure 4

• EDF 1.ipynb
• analysis-aml1.ipynb
• comparison-aml1-scvi-decipher.ipynb
• ext-fig-adjustments.ipynb

Figure 5

• analysis-aml1.ipynb
• temporal_tf.ipynb

Figure 6

• temporal_tf.ipynb
• cohort_comparison.ipynb

Figure 7

Supplementary Figure 1

• Figure_3_PDAC.ipynb
• pdac_scvi.ipynb

Supplementary Figure 2

• EDF 1.ipynb
• mutation_call.ipynb
• 00_decipher AML cohort.ipynb

Supplementary Figure 3

• ext-fig-adjustments.ipynb

Supplementary Figure 4

• benchmark/1-run-R-methods.ipynb
• benchmark/2-run-Python-methods.ipynb
• benchmark/3-evaluate-metric.ipynb

Supplementary Figure 5

• ext-fig-adjustments.ipynb

Supplementary Figure 6

Supplementary Figure 7

• temporal_tf.ipynb

Supplementary Figure 8

• temporal_tf.ipynb

Supplementary Figure 9

• temporal_tf.ipynb

Supplementary Figure 10

• temporal_tf.ipynb

Supplementary Figure 11

• cohort_comparison.ipynb
• <additional notebook?>

SI Figure 1

SI Figure 2

• RNA_ATAC_figures.ipynb
• LIGER_from_ARCHR_merged-AML7.ipynb
• Example_ArchR.ipynb

SI Figure 3

• RNA_ATAC_figures.ipynb