├── .gitignore ├── LICENSE ├── README.md ├── cytograph ├── README.md ├── __init__.py ├── _version.py ├── annotation │ ├── __init__.py │ ├── auto_annotator.py │ ├── auto_auto_annotator.py │ └── cell_cycle_annotator.py ├── clustering │ ├── __init__.py │ ├── cluster_validator.py │ ├── polished_louvain.py │ ├── polished_surprise.py │ └── unpolished_louvain.py ├── decomposition │ ├── HPF.py │ ├── HPF_accel.py │ ├── __init__.py │ ├── incremental_residuals_pca.py │ └── pca.py ├── embedding │ ├── __init__.py │ ├── art_of_tsne.py │ └── custom_init.py ├── enrichment │ ├── __init__.py │ ├── binary_differential_expression.py │ ├── enrichment.py │ ├── feature_selection_by_deviance.py │ ├── feature_selection_by_enrichment.py │ ├── feature_selection_by_multilevel_enrichment.py │ ├── feature_selection_by_variance.py │ ├── gsea.py │ ├── neighborhood_enrichment.py │ └── trinarizer.py ├── manifold │ ├── __init__.py │ ├── balanced_knn.py │ ├── graph_skeletonizer.py │ └── poisson_pooling.py ├── metrics │ ├── __init__.py │ ├── laplacian_score.py │ ├── poisson_proximity.py │ └── special_metrics.py ├── pipeline │ ├── __init__.py │ ├── aggregator.py │ ├── commands.py │ ├── config.py │ ├── cytograph.py │ ├── engine.py │ ├── punchcards.py │ ├── utils.py │ └── workflow.py ├── plotting │ ├── TF_heatmap.py │ ├── __init__.py │ ├── batch_covariates.py │ ├── buckets.py │ ├── cell_cycle.py │ ├── colors.py │ ├── decision_boundary.py │ ├── dendrogram.py │ ├── doublets_plots.py │ ├── embedded_velocity.py │ ├── factors.py │ ├── gene_velocity.py │ ├── heatmap.py │ ├── manifold.py │ ├── markerheatmap.py │ ├── metromap.py │ ├── midpoint_normalize.py │ ├── punchcard_selection.py │ ├── qc_plots.py │ ├── radius_characteristics.py │ ├── scatter.py │ └── umi_genes.py ├── postprocessing │ ├── __init__.py │ ├── merge_subset.py │ └── split_subset.py ├── preprocessing │ ├── __init__.py │ ├── doublet_finder.py │ ├── genotyping.py │ ├── normalizer.py │ ├── qc_functions.py │ └── utils.py ├── species │ ├── __init__.py │ ├── human.py │ ├── mouse.py │ └── species.py ├── utils.py └── visualization │ ├── __init__.py │ ├── colors.py │ ├── plot_overview.py │ └── scatter.py ├── notebooks ├── Preprint │ ├── Figure1.ipynb │ ├── Figure2.ipynb │ ├── Figure3.ipynb │ ├── Figure5.ipynb │ ├── Figure5_Diffxpy.ipynb │ ├── Figure6.ipynb │ ├── FigureS1.ipynb │ ├── FigureS10.ipynb │ ├── FigureS7.ipynb │ ├── ncRNA.txt │ └── roi_group_table.csv └── Revision │ ├── RebuttalFigures.ipynb │ ├── RevisionDiffExp.ipynb │ ├── RevisionFig2.ipynb │ ├── RevisionFig3andSupp.ipynb │ ├── RevisionFigS2-3.ipynb │ ├── RevisionFigS7_LDA.ipynb │ ├── RevisionPreprintFigs.ipynb │ └── TH_neurons │ ├── DA.ipynb │ ├── RF_params │ ├── metrics_train_mean_accuracy.csv │ ├── metrics_train_mean_f1.csv │ └── trials_params.csv │ ├── color.py │ ├── helper_utils.py │ ├── mplt.py │ └── scatterm.py ├── scripts ├── downsample_data.py ├── optimize_lda.py ├── permuted_pca.py ├── prepare_integration.py └── split.py ├── setup.cfg ├── setup.py └── tables ├── 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