├── .gitignore ├── README.md ├── cytograph ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── _version.cpython-37.pyc │ └── utils.cpython-37.pyc ├── _version.py ├── annotation │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── auto_annotator.cpython-37.pyc │ │ ├── auto_auto_annotator.cpython-37.pyc │ │ ├── cell_cycle_annotator.cpython-37.pyc │ │ └── karyotyper.cpython-37.pyc │ ├── auto_annotator.py │ ├── auto_auto_annotator.py │ └── cell_cycle_annotator.py ├── clustering │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── cluster_validator.cpython-37.pyc │ │ ├── louvain.cpython-37.pyc │ │ ├── polished_louvain.cpython-37.pyc │ │ └── polished_surprise.cpython-37.pyc │ ├── cluster_validator.py │ ├── polished_louvain.py │ └── polished_surprise.py ├── decomposition │ ├── HPF.py │ ├── HPF_accel.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── HPF_accel.cpython-37.pyc │ │ ├── __init__.cpython-37.pyc │ │ └── pca.cpython-37.pyc │ └── pca.py ├── embedding │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── art_of_tsne.cpython-37.pyc │ └── art_of_tsne.py ├── enrichment │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── feature_selection_by_enrichment.cpython-37.pyc │ │ ├── feature_selection_by_multilevel_enrichment.cpython-37.pyc │ │ ├── feature_selection_by_variance.cpython-37.pyc │ │ ├── gsea.cpython-37.pyc │ │ ├── neighborhood_enrichment.cpython-37.pyc │ │ └── trinarizer.cpython-37.pyc │ ├── feature_selection_by_enrichment.py │ ├── feature_selection_by_multilevel_enrichment.py │ ├── feature_selection_by_variance.py │ ├── gsea.py │ ├── neighborhood_enrichment.py │ └── trinarizer.py ├── interpolation │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ └── catmull_rom.cpython-37.pyc │ └── catmull_rom.py ├── manifold │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── balanced_knn.cpython-37.pyc │ │ ├── graph_skeletonizer.cpython-37.pyc │ │ ├── poisson_pooling.cpython-37.pyc │ │ ├── principal_curve.cpython-37.pyc │ │ └── pseudo_lineage.cpython-37.pyc │ ├── balanced_knn.py │ ├── graph_skeletonizer.py │ ├── poisson_pooling.py │ ├── principal_curve.py │ └── pseudo_lineage.py ├── metrics │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── poisson_proximity.cpython-37.pyc │ │ ├── special_metrics.cpython-37.pyc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.1.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.10.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.2.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.3.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.4.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.5.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.6.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.7.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.8.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.9.nbc │ │ ├── special_metrics.jensen_shannon_distance-55.py37m.nbi │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.1.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.10.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.2.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.3.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.4.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.5.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.6.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.7.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.8.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.9.nbc │ │ ├── special_metrics.jensen_shannon_divergence-25.py37m.nbi │ │ ├── special_metrics.kullback_leibler-8.py37m.1.nbc │ │ ├── special_metrics.kullback_leibler-8.py37m.2.nbc │ │ ├── special_metrics.kullback_leibler-8.py37m.3.nbc │ │ ├── special_metrics.kullback_leibler-8.py37m.4.nbc │ │ ├── special_metrics.kullback_leibler-8.py37m.5.nbc │ │ ├── special_metrics.kullback_leibler-8.py37m.nbi │ │ ├── special_metrics.minkowski10-86.py37m.1.nbc │ │ ├── special_metrics.minkowski10-86.py37m.2.nbc │ │ ├── special_metrics.minkowski10-86.py37m.3.nbc │ │ ├── special_metrics.minkowski10-86.py37m.4.nbc │ │ ├── special_metrics.minkowski10-86.py37m.5.nbc │ │ ├── special_metrics.minkowski10-86.py37m.nbi │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.1.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.10.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.2.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.3.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.4.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.5.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.6.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.7.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.8.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.9.nbc │ │ ├── special_metrics.multinomial_subspace_distance-104.py37m.nbi │ │ ├── special_metrics.stabilized_minkowski-77.py37m.1.nbc │ │ ├── special_metrics.stabilized_minkowski-77.py37m.2.nbc │ │ ├── special_metrics.stabilized_minkowski-77.py37m.3.nbc │ │ ├── special_metrics.stabilized_minkowski-77.py37m.4.nbc │ │ ├── special_metrics.stabilized_minkowski-77.py37m.5.nbc │ │ └── special_metrics.stabilized_minkowski-77.py37m.nbi │ ├── laplacian_score.py │ ├── poisson_proximity.py │ └── special_metrics.py ├── pipeline │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── aggregator.cpython-37.pyc │ │ ├── commands.cpython-37.pyc │ │ ├── config.cpython-37.pyc │ │ ├── cytograph.cpython-37.pyc │ │ ├── engine.cpython-37.pyc │ │ ├── punchcards.cpython-37.pyc │ │ ├── utils.cpython-37.pyc │ │ └── workflow.cpython-37.pyc │ ├── aggregator.py │ ├── commands.py │ ├── config.py │ ├── cytograph.py │ ├── engine.py │ ├── punchcards.py │ ├── utils.py │ └── workflow.py ├── plotting │ ├── TF_heatmap.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── TF_heatmap.cpython-37.pyc │ │ ├── __init__.cpython-37.pyc │ │ ├── batch_covariates.cpython-37.pyc │ │ ├── buckets.cpython-37.pyc │ │ ├── cell_cycle.cpython-37.pyc │ │ ├── colors.cpython-37.pyc │ │ ├── decision_boundary.cpython-37.pyc │ │ ├── dendrogram.cpython-37.pyc │ │ ├── doublets_plots.cpython-37.pyc │ │ ├── embedded_velocity.cpython-37.pyc │ │ ├── factors.cpython-37.pyc │ │ ├── gene_velocity.cpython-37.pyc │ │ ├── heatmap.cpython-37.pyc │ │ ├── manifold.cpython-37.pyc │ │ ├── markerheatmap.cpython-37.pyc │ │ ├── metromap.cpython-37.pyc │ │ ├── midpoint_normalize.cpython-37.pyc │ │ ├── punchcard_selection.cpython-37.pyc │ │ ├── qc_plots.cpython-37.pyc │ │ ├── radius_characteristics.cpython-37.pyc │ │ ├── scatter.cpython-37.pyc │ │ └── umi_genes.cpython-37.pyc │ ├── batch_covariates.py │ ├── buckets.py │ ├── cell_cycle.py │ ├── colors.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 │ └── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── merge_subset.cpython-37.pyc │ │ └── split_subset.cpython-37.pyc ├── preprocessing │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── batch_correction.cpython-37.pyc │ │ ├── doublet_finder.cpython-37.pyc │ │ ├── normalizer.cpython-37.pyc │ │ ├── qc_functions.cpython-37.pyc │ │ ├── scrublet.cpython-37.pyc │ │ └── utils.cpython-37.pyc │ ├── doublet_finder.py │ ├── normalizer.py │ ├── qc_functions.py │ └── utils.py ├── species │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── human.cpython-37.pyc │ │ ├── mouse.cpython-37.pyc │ │ └── species.cpython-37.pyc │ ├── human.py │ ├── mouse.py │ └── species.py └── utils.py ├── debug.py ├── doc ├── Makefile ├── conf.py └── index.rst ├── setup.cfg └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | /.mypy_cache 2 | /.vscode 3 | /cytograph.egg-info -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linnarsson-lab/cytograph2/HEAD/README.md -------------------------------------------------------------------------------- /cytograph/__init__.py: -------------------------------------------------------------------------------- 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