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