├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── demo.ipynb ├── environment.yml ├── models ├── __init__.py ├── cf.py ├── likelihoods.py ├── mefisto.py ├── sf.py └── sfh.py ├── nsf-paper.Rproj ├── requirements.txt ├── scrna ├── .gitignore ├── 01_viz_spatial_importance.Rmd ├── sshippo │ ├── 01_data_loading.Rmd │ ├── 02_data_loading.ipy │ ├── 03_benchmark.ipy │ ├── 04_exploratory.ipy │ ├── 05_benchmark_viz.Rmd │ ├── 06_interpret_genes.Rmd │ ├── 07_traditional.ipy │ └── results │ │ └── benchmark.csv ├── utils │ └── interpret_genes.R ├── visium_brain_sagittal │ ├── 01_data_loading.ipy │ ├── 02_exploratory.ipy │ ├── 03_benchmark.ipy │ ├── 04_benchmark_viz.Rmd │ ├── 05_interpret_genes.Rmd │ ├── 06_traditional.ipy │ └── results │ │ └── benchmark.csv └── xyzeq_liver │ ├── 01_data_loading.ipy │ ├── 02_exploratory.ipy │ ├── 03_benchmark.ipy │ ├── 04_benchmark_viz.Rmd │ ├── 05_interpret_genes.Rmd │ ├── 06_traditional.ipy │ └── results │ └── benchmark.csv ├── simulations ├── .gitignore ├── __init__.py ├── benchmark.py ├── benchmark.slurm ├── benchmark_gof.py ├── benchmark_gof.slurm ├── bm_mixed │ ├── 01_data_generation.ipy │ ├── 02_benchmark.ipy │ ├── 03_benchmark_viz.Rmd │ └── results │ │ └── benchmark.csv ├── bm_sp │ ├── 01_data_generation.ipy │ ├── 02_benchmark.ipy │ ├── 03_benchmark_viz.Rmd │ ├── 04_quilt_exploratory.ipy │ ├── 05_ggblocks_exploratory.ipy │ ├── data │ │ ├── S1.h5ad │ │ └── S6.h5ad │ └── results │ │ └── benchmark.csv └── sim.py └── utils ├── __init__.py ├── benchmark.py ├── benchmark_array.slurm ├── benchmark_gof.py ├── benchmark_gof.slurm ├── misc.py ├── nnfu.py ├── postprocess.py ├── preprocess.py ├── training.py └── visualize.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/willtownes/nsf-paper/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: 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