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:

https://github.com/azizilab/decipher at commit: 63b7d25c44bf1bbfa65ca7865e41b6c9b0abcf07.
https://github.com/azizilab/decipher/releases/tag/reproducibility at tag: reproducibility.
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