├── .cruft.json ├── .editorconfig ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── general_question.yml ├── labels.yml ├── pull_request_template.md ├── release-drafter.yml └── workflows │ ├── build.yml │ ├── labeler.yml │ ├── release.yml │ ├── release_drafter.yml │ ├── run_notebooks.yml │ └── test.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── biome.jsonc ├── codecov.yml ├── docs ├── Makefile ├── _ext │ ├── edit_on_github.py │ └── typed_returns.py ├── _static │ ├── css │ │ ├── overwrite.css │ │ └── sphinx_gallery.css │ ├── docstring_previews │ │ ├── catplot.png │ │ ├── clustermap.png │ │ ├── cohort_tracking.png │ │ ├── coxph_forestplot.png │ │ ├── dendrogram.png │ │ ├── diffmap.png │ │ ├── dotplot.png │ │ ├── dpt_groups_pseudotime.png │ │ ├── dpt_timeseries.png │ │ ├── draw_graph_1.png │ │ ├── draw_graph_2.png │ │ ├── embedding.png │ │ ├── embedding_density.png │ │ ├── feature_importances.png │ │ ├── flowchart.png │ │ ├── heatmap.png │ │ ├── kmf_plot_1.png │ │ ├── kmf_plot_2.png │ │ ├── matrixplot.png │ │ ├── missingno_barplot.png │ │ ├── missingno_dendrogram.png │ │ ├── missingno_heatmap.png │ │ ├── missingno_matrix.png │ │ ├── ols_plot.png │ │ ├── paga.png │ │ ├── pca.png │ │ ├── pca_loadings.png │ │ ├── pca_overview_1.png │ │ ├── pca_overview_2.png │ │ ├── pca_overview_3.png │ │ ├── pca_variance_ratio.png │ │ ├── rank_features_groups.png │ │ ├── rank_features_groups_dotplot.png │ │ ├── rank_features_groups_heatmap.png │ │ ├── rank_features_groups_matrixplot.png │ │ ├── rank_features_groups_stacked_violin.png │ │ ├── rank_features_groups_tracksplot.png │ │ ├── rank_features_groups_violin_1.png │ │ ├── rank_features_groups_violin_2.png │ │ ├── rank_features_groups_violin_3.png │ │ ├── rank_features_groups_violin_4.png │ │ ├── scatter.png │ │ ├── stacked_violin.png │ │ ├── tracksplot.png │ │ ├── tsne_1.png │ │ ├── tsne_2.png │ │ ├── tsne_3.png │ │ ├── umap_1.png │ │ ├── umap_2.png │ │ ├── umap_3.png │ │ └── violin.png │ ├── ehrapy_logos │ │ ├── ehrapy_logo.png │ │ ├── ehrapy_logo_wide.png │ │ ├── ehrapy_logo_wide_2.png │ │ ├── ehrapy_pure.png │ │ ├── nat_med_cover_no_text_compressed.png │ │ ├── nat_med_cover_upscaled.png │ │ └── nat_med_cover_upscaled_compressed.png │ ├── icons │ │ ├── code-24px.svg │ │ ├── computer-24px.svg │ │ ├── library_books-24px.svg │ │ └── play_circle_outline-24px.svg │ ├── overview.png │ └── tutorials │ │ ├── bias.png │ │ ├── catheter.png │ │ ├── causal_inference.png │ │ ├── cohort_tracking.png │ │ ├── effect_estimation.png │ │ ├── fate.png │ │ ├── fhir.png │ │ ├── machine_learning.png │ │ ├── nlp.png │ │ ├── ontology.png │ │ ├── out_of_core.png │ │ ├── patient_trajectory.png │ │ ├── placeholder.png │ │ └── survival.png ├── _templates │ └── autosummary │ │ └── class.rst ├── about │ ├── background.md │ └── cite.md ├── api.md ├── api │ ├── anndata_index.md │ ├── datasets_index.md │ ├── io_index.md │ ├── plot_index.md │ ├── preprocessing_index.md │ ├── settings_index.md │ └── tools_index.md ├── changelog.md ├── conf.py ├── contributing.md ├── index.md ├── installation.md ├── make.bat ├── references.bib ├── references.md ├── tutorials │ └── index.md └── utils.py ├── ehrapy ├── SCANPY_LICENSE ├── __init__.py ├── _compat.py ├── _progress.py ├── _settings.py ├── _types.py ├── _utils_doc.py ├── anndata │ ├── __init__.py │ ├── _feature_specifications.py │ └── anndata_ext.py ├── core │ ├── __init__.py │ ├── _constants.py │ └── meta_information.py ├── data │ ├── __init__.py │ ├── _dataloader.py │ └── _datasets.py ├── get │ ├── __init__.py │ └── _get.py ├── io │ ├── __init__.py │ ├── _read.py │ └── _write.py ├── plot │ ├── __init__.py │ ├── _catplot.py │ ├── _colormaps.py │ ├── _missingno.py │ ├── _scanpy_pl_api.py │ ├── _survival_analysis.py │ ├── causal_inference │ │ ├── __init__.py │ │ └── _dowhy.py │ └── feature_ranking │ │ ├── __init__.py │ │ └── _feature_importances.py ├── preprocessing │ ├── __init__.py │ ├── _balanced_sampling.py │ ├── _bias.py │ ├── _encoding.py │ ├── _filter.py │ ├── _highly_variable_features.py │ ├── _imputation.py │ ├── _neighbors.py │ ├── _normalization.py │ ├── _outliers.py │ ├── _quality_control.py │ ├── _scanpy_pp_api.py │ ├── _summarize_measurements.py │ └── laboratory_reference_tables │ │ └── laposata.tsv ├── py.typed └── tools │ ├── __init__.py │ ├── _method_options.py │ ├── _sa.py │ ├── _scanpy_tl_api.py │ ├── causal │ ├── __init__.py │ └── _dowhy.py │ ├── cohort_tracking │ ├── __init__.py │ └── _cohort_tracker.py │ ├── distances │ ├── __init__.py │ └── timeseries.py │ ├── embedding │ └── _embeddings.py │ └── feature_ranking │ ├── __init__.py │ ├── _feature_importances.py │ └── _rank_features_groups.py ├── pyproject.toml └── tests ├── __init__.py ├── _scripts ├── catplot_create_expected_plots.ipynb ├── clustermap_scanpy_expected.ipynb ├── cohort_tracker_test_create_expected_plots.ipynb ├── coxph_forestplot_create_expected.ipynb ├── dendogram_expected.ipynb ├── diffmap_expected.ipynb ├── dotplot_scanpy_plt_expected.ipynb ├── dpt_groups_pseudotime_expected.ipynb ├── dpt_timeseries_expected.ipynb ├── draw_graph_expected.ipynb ├── dtw_test_reference.ipynb ├── embedding_density_expected.ipynb ├── embedding_expected.ipynb ├── heatmap_scanpy_plt_expected.ipynb ├── kaplain_meier_create_expected_plots.ipynb ├── matrix_scanpy_plot_expected.ipynb ├── missing_values_barplot_expected.ipynb ├── missing_values_dendogram_dendogram.ipynb ├── missing_values_heatmap_expected.ipynb ├── missing_values_matrix_expected.ipynb ├── ols_expected.ipynb ├── paga_expected copy.ipynb ├── paga_expected.ipynb ├── pca_loadings_expected.ipynb ├── pca_overview_expected.ipynb ├── pca_scanpy_expected.ipynb ├── pca_variance_ratio_expected.ipynb ├── rank_features_groups_dotplot_expected.ipynb ├── rank_features_groups_expected.ipynb ├── rank_features_groups_heatmap_expected.ipynb ├── rank_features_groups_matrixplot_expected.ipynb ├── rank_features_groups_stacked_violin_expected.ipynb ├── rank_features_groups_tracksplot_expected.ipynb ├── rank_features_groups_violin_expected.ipynb ├── scatter_scanpy_plt_expected.ipynb ├── stacked_violin_scanpy_plt_expected.ipynb ├── tracksplot_expected.ipynb ├── tsne_expected.ipynb ├── umap_expected.ipynb └── violin_scanpy_plt_expected.ipynb ├── anndata ├── __init__.py ├── test_anndata_ext.py └── test_feature_specifications.py ├── conftest.py ├── core └── test_print_versions.py ├── data ├── dataset1.csv ├── encode │ ├── dataset1.csv │ └── dataset2.csv ├── imputation │ ├── test_impute.csv │ ├── test_impute_iris.csv │ ├── test_impute_num.csv │ └── test_impute_titanic.csv └── io │ ├── dataset_basic.csv │ ├── dataset_bools_and_str.csv │ ├── dataset_index.csv │ ├── dataset_move_obs_mix.csv │ ├── dataset_move_obs_num.csv │ ├── dataset_non_num_with_missing.csv │ ├── dataset_num_with_missing.csv │ ├── dataset_tsv.tsv │ ├── fhir │ └── json │ │ ├── 746cb231-3273-434a-9da4-b12c20862b1e.json │ │ ├── README.md │ │ ├── a5811ae4-e151-4d80-9021-743b38cab86b.json │ │ ├── hospitalInformation1582751636531.json │ │ └── practitionerInformation1582751636531.json │ └── h5ad │ ├── dataset8.h5ad │ └── dataset9.h5ad ├── get └── test_get.py ├── io └── test_read.py ├── plot ├── _images │ ├── catplot_vanilla_expected.png │ ├── clustermap_scanpy_expected.png │ ├── coxph_forestplot_expected.png │ ├── dendogram_expected.png │ ├── diffmap_expected.png │ ├── dotplot_scanpy_plt_expected.png │ ├── dpt_timeseries_expected.png │ ├── draw_graph1_expected.png │ ├── draw_graph2_expected.png │ ├── embedding_density_expected.png │ ├── embedding_expected.png │ ├── embedding_test_output.png │ ├── heatmap_scanpy_plt_expected.png │ ├── kaplan_meier_expected.png │ ├── kaplan_meier_table_expected.png │ ├── matrix_scanpy_plot_expected.png │ ├── missing_values_barplot_expected.png │ ├── missing_values_dendogram_expected.png │ ├── missing_values_heatmap_expected.png │ ├── missing_values_matrix_expected.png │ ├── paga_control_expected.png │ ├── paga_expected.png │ ├── paga_production.png │ ├── pca_expected.png │ ├── pca_loadings_expected.png │ ├── pca_overview_1_expected.png │ ├── pca_overview_2_expected.png │ ├── pca_overview_3_expected.png │ ├── pca_overview_expected.png │ ├── pca_variance_ratio_expected.png │ ├── rank_features_groups_dotplot_scanpy_expected.png │ ├── rank_features_groups_heatmap_scanpy_expected.png │ ├── rank_features_groups_matrixplot_scanpy_expected.png │ ├── rank_features_groups_scanpy_plt_expected.png │ ├── rank_features_groups_stacked_violin_scanpy_expected.png │ ├── rank_features_groups_tracksplot_scanpy_expected.png │ ├── rank_features_groups_violin_expected.png │ ├── scatter_scanpy_plt_expected.png │ ├── stacked_violin_scanpy_plt_expected.png │ ├── tracksplot_scanpy_plt_expected.png │ ├── tsne_expected.png │ ├── umap_expected.png │ └── violin_scanpy_plt_expected.png ├── test_catplot.py ├── test_missingno_pl_api.py ├── test_scanpy_pl_api.py └── test_survival_analysis.py ├── preprocessing ├── test_balanced_sampling.py ├── test_bias.py ├── test_encoding.py ├── test_filter.py ├── test_highly_variable_features.py ├── test_imputation.py ├── test_neighbors.py ├── test_normalization.py ├── test_outliers.py ├── test_quality_control.py ├── test_scanpy_pp_api.py └── test_summarize_measurements.py ├── test_compat.py ├── tools ├── __init__.py ├── _images │ ├── cohorttracker_edata_mini_flowchart_expected.png │ ├── cohorttracker_edata_mini_step1_use_settings_big_expected.png │ ├── cohorttracker_edata_mini_step1_use_settings_expected.png │ ├── cohorttracker_edata_mini_step1_vanilla_expected.png │ ├── cohorttracker_edata_mini_step2_loose_category_expected.png │ └── cohorttracker_edata_mini_step2_vanilla_expected.png ├── causal │ └── test_dowhy.py ├── cohort_tracking │ └── test_cohort_tracking.py ├── distances │ └── test_timeseries.py 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