├── .dockerignore ├── .gitattributes ├── .github └── workflows │ └── build-test.yml ├── .gitignore ├── .gitmodules ├── Dockerfile ├── LICENSE ├── PyCoGAPS ├── __init__.py ├── analysis_functions.py ├── config.py ├── distributed_functions.py ├── helper_functions.py ├── msigdb_gsea.py ├── parameters.py ├── pycogaps_main.py ├── requirements_analysis.txt ├── run_pycogaps.py └── subset_data.py ├── README.md ├── analyzepdac.py ├── analyzevisium.py ├── data ├── GIST.csv ├── ModSimBases.txt ├── ModSimData.txt ├── ModSimResult.h5ad ├── cogapsresult.h5ad └── inputdata.h5ad ├── figures ├── highest_expr_genes_highestExpressedGenes.png ├── pdac1kpatternumap.png └── umap_UMAP.png ├── genepattern └── Dockerfile ├── modsimvignette.py ├── params.yaml ├── pdacvignette.py ├── readme-figs ├── anndata-result.jpeg ├── anndata-result.png ├── binaryA.png ├── binaryA_cluster.png ├── plot_pm.png ├── plot_residuals.png └── res_show.png ├── requirements.txt ├── run_vignette.sh ├── setup.py ├── src └── bindings.cpp ├── tests ├── read_pydata.py ├── test_checkpoints.py ├── test_distributed.py ├── test_disttime.py ├── test_params.py ├── test_pytime.py ├── test_r_time.R ├── test_retina.py ├── test_seed_consistency.py ├── test_subsets.py ├── test_top_level.py └── testing.py ├── vignette.py ├── vignette_from_args.py └── visiumvignette.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FertigLab/pycogaps/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FertigLab/pycogaps/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/build-test.yml: -------------------------------------------------------------------------------- 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