├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ ├── css │ │ └── custom.css │ └── images │ │ ├── any.png │ │ └── scanpy.png ├── api.rst ├── authors.rst ├── conf.py ├── images │ └── logo.png ├── index.rst ├── installation.rst ├── interactive.rst ├── make.bat ├── references.rst ├── release_notes │ ├── 0.3.2.rst │ ├── 0.4.6.rst │ ├── 1.1.1.rst │ ├── 1.1.5.rst │ ├── 1.2.2.rst │ └── index.rst └── tutorials.rst ├── mypy.ini ├── pyproject.toml ├── requirements.txt ├── resource ├── README.md ├── connectomedb2020.txt ├── label_transfer_bc.csv ├── means.txt └── predictions.csv ├── stlearn ├── __init__.py ├── __main__.py ├── _datasets │ ├── __init__.py │ └── _datasets.py ├── _settings.py ├── add.py ├── adds │ ├── __init__.py │ ├── add_deconvolution.py │ ├── add_image.py │ ├── add_labels.py │ ├── add_loupe_clusters.py │ ├── add_lr.py │ ├── add_mask.py │ ├── add_positions.py │ ├── annotation.py │ └── parsing.py ├── app │ ├── __init__.py │ ├── app.py │ ├── cli.py │ ├── requirements.txt │ ├── source │ │ ├── __init__.py │ │ ├── forms │ │ │ ├── __init__.py │ │ │ ├── form_validators.py │ │ │ ├── forms.py │ │ │ ├── helper_functions.py │ │ │ ├── utils.py │ │ │ ├── view_helpers.py │ │ │ └── views.py │ │ └── readme.md │ ├── static │ │ ├── css │ │ │ ├── material-dashboard.min.css │ │ │ └── style.css │ │ ├── img │ │ │ ├── Settings.gif │ │ │ ├── favicon.png │ │ │ └── loading_gif.gif │ │ └── js │ │ │ ├── core │ │ │ ├── bootstrap-material-design.min.js │ │ │ ├── jquery.min.js │ │ │ └── popper.min.js │ │ │ └── plugins │ │ │ └── perfect-scrollbar.jquery.min.js │ └── templates │ │ ├── __init__.py │ │ ├── annotate_plot.html │ │ ├── base.html │ │ ├── cci.html │ │ ├── cci_old.html │ │ ├── cci_plot.html │ │ ├── choose_cluster.html │ │ ├── cluster_plot.html │ │ ├── clustering.html │ │ ├── dea.html │ │ ├── flash_header.html │ │ ├── gene_plot.html │ │ ├── index.html │ │ ├── lr.html │ │ ├── lr_plot.html │ │ ├── preprocessing.html │ │ ├── progress.html │ │ ├── psts.html │ │ ├── spatial_cci_plot.html │ │ ├── superform.html │ │ └── upload.html ├── classes.py ├── datasets.py ├── em.py ├── embedding │ ├── __init__.py │ ├── diffmap.py │ ├── fa.py │ ├── ica.py │ ├── pca.py │ └── umap.py ├── gui.py ├── image_preprocessing │ ├── __init__.py │ ├── feature_extractor.py │ ├── image_tiling.py │ └── model_zoo.py ├── logging.py ├── pl │ ├── QC_plot.py │ ├── __init__.py │ ├── _docs.py │ ├── cci_plot.py │ ├── cci_plot_helpers.py │ ├── classes.py │ ├── classes_bokeh.py │ ├── cluster_plot.py │ ├── deconvolution_plot.py │ ├── feat_plot.py │ ├── gene_plot.py │ ├── mask_plot.py │ ├── non_spatial_plot.py │ ├── palettes_st.py │ ├── stack_3d_plot.py │ ├── subcluster_plot.py │ ├── trajectory │ │ ├── DE_transition_plot.py │ │ ├── __init__.py │ │ ├── check_trajectory.py │ │ ├── local_plot.py │ │ ├── pseudotime_plot.py │ │ ├── transition_markers_plot.py │ │ ├── tree_plot.py │ │ ├── tree_plot_simple.py │ │ └── utils.py │ └── utils.py ├── pp.py ├── preprocessing │ ├── __init__.py │ ├── filter_cells.py │ ├── filter_genes.py │ ├── graph.py │ ├── log_scale.py │ └── normalize.py ├── spatial │ ├── SME │ │ ├── __init__.py │ │ ├── _weighting_matrix.py │ │ ├── pseudo_spot.py │ │ ├── sme_impute0.py │ │ └── sme_normalize.py │ ├── __init__.py │ ├── clustering │ │ ├── __init__.py │ │ └── localization.py │ ├── morphology │ │ ├── __init__.py │ │ └── adjust.py │ ├── smooth │ │ ├── __init__.py │ │ └── disk.py │ └── trajectory │ │ ├── __init__.py │ │ ├── compare_transitions.py │ │ ├── detect_transition_markers.py │ │ ├── global_level.py │ │ ├── local_level.py │ │ ├── pseudotime.py │ │ ├── pseudotimespace.py │ │ ├── set_root.py │ │ ├── shortest_path_spatial_PAGA.py │ │ ├── utils.py │ │ └── weight_optimization.py ├── tl │ ├── __init__.py │ ├── cache │ │ ├── __init__.py │ │ └── anndata.py │ ├── cci │ │ ├── __init__.py │ │ ├── analysis.py │ │ ├── base.py │ │ ├── base_grouping.py │ │ ├── databases │ │ │ ├── __init__.py │ │ │ ├── connectomeDB2020_lit.txt │ │ │ └── connectomeDB2020_put.txt │ │ ├── go.R │ │ ├── go.py │ │ ├── het.py │ │ ├── het_helpers.py │ │ ├── merge.py │ │ ├── perm_utils.py │ │ ├── permutation.py │ │ └── r_helpers.py │ ├── clustering │ │ ├── __init__.py │ │ ├── annotate.py │ │ ├── kmeans.py │ │ ├── leiden.py │ │ └── louvain.py │ └── label │ │ ├── __init__.py │ │ ├── label.py │ │ ├── label_transfer.R │ │ ├── rctd.R │ │ └── singleR.R ├── types.py ├── utils.py └── wrapper │ ├── __init__.py │ ├── concatenate_spatial_adata.py │ ├── convert_scanpy.py │ ├── read.py │ └── xenium_alignment.py ├── tests ├── __init__.py ├── test_CCI.py ├── test_PSTS.py ├── test_SME.py ├── test_Spatial.py ├── test_cluster_plot.py ├── test_data │ ├── test_data.h5 │ └── test_image.jpg ├── test_extract_features.py ├── test_tiling.py ├── test_tools.py └── utils.py └── tox.ini 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