.azure-pipelines.yml
LICENSE
MANIFEST.in
README.rst
conftest.py
pyproject.toml
requirements.txt
setup.py
.github/pull_request_template.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/enhancement-request.md
.github/ISSUE_TEMPLATE/question.md
scanpy/__init__.py
scanpy/__main__.py
scanpy/_compat.py
scanpy/_metadata.py
scanpy/_settings.py
scanpy/_utils.py
scanpy/cli.py
scanpy/logging.py
scanpy/readwrite.py
scanpy.egg-info/PKG-INFO
scanpy.egg-info/SOURCES.txt
scanpy.egg-info/dependency_links.txt
scanpy.egg-info/entry_points.txt
scanpy.egg-info/not-zip-safe
scanpy.egg-info/requires.txt
scanpy.egg-info/top_level.txt
scanpy/api/__init__.py
scanpy/api/datasets.py
scanpy/api/export_to.py
scanpy/api/logging.py
scanpy/api/pl.py
scanpy/api/pp.py
scanpy/api/queries.py
scanpy/api/tl.py
scanpy/datasets/10x_pbmc68k_reduced.h5ad
scanpy/datasets/__init__.py
scanpy/datasets/_datasets.py
scanpy/datasets/_ebi_expression_atlas.py
scanpy/datasets/_utils.py
scanpy/datasets/krumsiek11.txt
scanpy/datasets/toggleswitch.txt
scanpy/external/__init__.py
scanpy/external/exporting.py
scanpy/external/pl.py
scanpy/external/pp/__init__.py
scanpy/external/pp/_bbknn.py
scanpy/external/pp/_dca.py
scanpy/external/pp/_harmony_integrate.py
scanpy/external/pp/_hashsolo.py
scanpy/external/pp/_magic.py
scanpy/external/pp/_mnn_correct.py
scanpy/external/pp/_scanorama_integrate.py
scanpy/external/pp/_scrublet.py
scanpy/external/pp/_scvi.py
scanpy/external/tl/__init__.py
scanpy/external/tl/_harmony_timeseries.py
scanpy/external/tl/_palantir.py
scanpy/external/tl/_phate.py
scanpy/external/tl/_phenograph.py
scanpy/external/tl/_pypairs.py
scanpy/external/tl/_sam.py
scanpy/external/tl/_trimap.py
scanpy/external/tl/_wishbone.py
scanpy/get/__init__.py
scanpy/get/get.py
scanpy/neighbors/__init__.py
scanpy/plotting/__init__.py
scanpy/plotting/_anndata.py
scanpy/plotting/_baseplot_class.py
scanpy/plotting/_docs.py
scanpy/plotting/_dotplot.py
scanpy/plotting/_matrixplot.py
scanpy/plotting/_preprocessing.py
scanpy/plotting/_qc.py
scanpy/plotting/_rcmod.py
scanpy/plotting/_stacked_violin.py
scanpy/plotting/_utils.py
scanpy/plotting/palettes.py
scanpy/plotting/_tools/__init__.py
scanpy/plotting/_tools/paga.py
scanpy/plotting/_tools/scatterplots.py
scanpy/preprocessing/__init__.py
scanpy/preprocessing/_combat.py
scanpy/preprocessing/_distributed.py
scanpy/preprocessing/_docs.py
scanpy/preprocessing/_highly_variable_genes.py
scanpy/preprocessing/_normalization.py
scanpy/preprocessing/_pca.py
scanpy/preprocessing/_qc.py
scanpy/preprocessing/_recipes.py
scanpy/preprocessing/_simple.py
scanpy/preprocessing/_utils.py
scanpy/preprocessing/_deprecated/__init__.py
scanpy/preprocessing/_deprecated/highly_variable_genes.py
scanpy/queries/__init__.py
scanpy/queries/_queries.py
scanpy/sim_models/__init__.py
scanpy/sim_models/krumsiek11.txt
scanpy/sim_models/krumsiek11_params.txt
scanpy/sim_models/toggleswitch.txt
scanpy/sim_models/toggleswitch_params.txt
scanpy/tests/blackdiff.py
scanpy/tests/conftest.py
scanpy/tests/fixtures.py
scanpy/tests/helpers.py
scanpy/tests/test_binary.py
scanpy/tests/test_clustering.py
scanpy/tests/test_combat.py
scanpy/tests/test_datasets.py
scanpy/tests/test_dendrogram_key_added.py
scanpy/tests/test_docs.py
scanpy/tests/test_embedding.py
scanpy/tests/test_embedding_density.py
scanpy/tests/test_embedding_plots.py
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scanpy/tests/test_get.py
scanpy/tests/test_highly_variable_genes.py
scanpy/tests/test_ingest.py
scanpy/tests/test_logging.py
scanpy/tests/test_marker_gene_overlap.py
scanpy/tests/test_neighbors.py
scanpy/tests/test_neighbors_key_added.py
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scanpy/tests/test_pca.py
scanpy/tests/test_performance.py
scanpy/tests/test_plotting.py
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scanpy/tests/test_queries.py
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scanpy/tests/test_read_10x.py
scanpy/tests/test_readwrite.py
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scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_data-vbound.numbers].png
scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_data-vbound.percentile].png
scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_data-vbounds.default].png
scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_right-vbound.numbers].png
scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_right-vbound.percentile].png
scanpy/tests/_images/embedding-missing-values/test_missing_values_continuous[spatial-na_color.default-legend.on_right-vbounds.default].png
scanpy/tests/_scripts/scanpy-testbin
scanpy/tests/_scripts/seurat_extract_hvg.r
scanpy/tests/_scripts/seurat_extract_hvg_v3.r
scanpy/tests/_scripts/seurat_hvg.csv
scanpy/tests/_scripts/seurat_hvg_v3.csv.gz
scanpy/tests/_scripts/seurat_hvg_v3_batch.csv
scanpy/tests/external/test_harmony_integrate.py
scanpy/tests/external/test_harmony_timeseries.py
scanpy/tests/external/test_hashsolo.py
scanpy/tests/external/test_magic.py
scanpy/tests/external/test_palantir.py
scanpy/tests/external/test_phenograph.py
scanpy/tests/external/test_sam.py
scanpy/tests/external/test_scanorama_integrate.py
scanpy/tests/external/test_scrublet.py
scanpy/tests/external/test_scvi.py
scanpy/tests/external/test_wishbone.py
scanpy/tests/notebooks/test_paga_paul15_subsampled.py
scanpy/tests/notebooks/test_pbmc3k.py
scanpy/tests/notebooks/_images_paga_paul15_subsampled/paga.png
scanpy/tests/notebooks/_images_paga_paul15_subsampled/paga_path.png
scanpy/tests/notebooks/pbmc3k_images/filter_genes_dispersion.png
scanpy/tests/notebooks/pbmc3k_images/highest_expr_genes.png
scanpy/tests/notebooks/pbmc3k_images/pca.png
scanpy/tests/notebooks/pbmc3k_images/pca_variance_ratio.png
scanpy/tests/notebooks/pbmc3k_images/rank_genes_groups_1.png
scanpy/tests/notebooks/pbmc3k_images/rank_genes_groups_2.png
scanpy/tests/notebooks/pbmc3k_images/rank_genes_groups_3.png
scanpy/tests/notebooks/pbmc3k_images/rank_genes_groups_4.png
scanpy/tests/notebooks/pbmc3k_images/scatter_1.png
scanpy/tests/notebooks/pbmc3k_images/scatter_2.png
scanpy/tests/notebooks/pbmc3k_images/scatter_3.png
scanpy/tests/notebooks/pbmc3k_images/violin.png
scanpy/tests/notebooks/pbmc3k_images/violin_2.png
scanpy/tools/__init__.py
scanpy/tools/_dendrogram.py
scanpy/tools/_diffmap.py
scanpy/tools/_dpt.py
scanpy/tools/_draw_graph.py
scanpy/tools/_embedding_density.py
scanpy/tools/_ingest.py
scanpy/tools/_leiden.py
scanpy/tools/_louvain.py
scanpy/tools/_marker_gene_overlap.py
scanpy/tools/_paga.py
scanpy/tools/_pca.py
scanpy/tools/_rank_genes_groups.py
scanpy/tools/_score_genes.py
scanpy/tools/_sim.py
scanpy/tools/_top_genes.py
scanpy/tools/_tsne.py
scanpy/tools/_tsne_fix.py
scanpy/tools/_umap.py
scanpy/tools/_utils.py
scanpy/tools/_utils_clustering.py