.gitignore
.pre-commit-config.yaml
.readthedocs.yml
AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
tox.ini
.github/workflows/pre-commit.yml
.github/workflows/python-package.yml
.github/workflows/python-publish.yml
stlearn/__init__.py
stlearn/__main__.py
stlearn/_compat.py
stlearn/_settings.py
stlearn/add.py
stlearn/classes.py
stlearn/datasets.py
stlearn/em.py
stlearn/logging.py
stlearn/pl.py
stlearn/pp.py
stlearn/spatial.py
stlearn/tl.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/not-zip-safe
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/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/plotting/QC_plot.py
stlearn/plotting/__init__.py
stlearn/plotting/_docs.py
stlearn/plotting/cci_plot.py
stlearn/plotting/classes.py
stlearn/plotting/classes_bokeh.py
stlearn/plotting/cluster_plot.py
stlearn/plotting/deconvolution_plot.py
stlearn/plotting/gene_plot.py
stlearn/plotting/mask_plot.py
stlearn/plotting/non_spatial_plot.py
stlearn/plotting/palettes_st.py
stlearn/plotting/subcluster_plot.py
stlearn/plotting/utils.py
stlearn/plotting/trajectory/DE_transition_plot.py
stlearn/plotting/trajectory/__init__.py
stlearn/plotting/trajectory/local_plot.py
stlearn/plotting/trajectory/pseudotime_plot.py
stlearn/plotting/trajectory/transition_markers_plot.py
stlearn/plotting/trajectory/tree_plot.py
stlearn/plotting/trajectory/utils.py
stlearn/preprocessing/__init__.py
stlearn/preprocessing/filter_genes.py
stlearn/preprocessing/graph.py
stlearn/preprocessing/log_scale.py
stlearn/preprocessing/normalize.py
stlearn/spatials/__init__.py
stlearn/spatials/SME/__init__.py
stlearn/spatials/SME/_weighting_matrix.py
stlearn/spatials/SME/impute.py
stlearn/spatials/SME/normalize.py
stlearn/spatials/clustering/__init__.py
stlearn/spatials/clustering/localization.py
stlearn/spatials/morphology/__init__.py
stlearn/spatials/morphology/adjust.py
stlearn/spatials/smooth/__init__.py
stlearn/spatials/smooth/disk.py
stlearn/spatials/trajectory/__init__.py
stlearn/spatials/trajectory/compare_transitions.py
stlearn/spatials/trajectory/detect_transition_markers.py
stlearn/spatials/trajectory/global_level.py
stlearn/spatials/trajectory/local_level.py
stlearn/spatials/trajectory/pseudotime.py
stlearn/spatials/trajectory/pseudotimespace.py
stlearn/spatials/trajectory/utils.py
stlearn/spatials/trajectory/weight_optimization.py
stlearn/tools/__init__.py
stlearn/tools/clustering/__init__.py
stlearn/tools/clustering/kmeans.py
stlearn/tools/clustering/louvain.py
stlearn/tools/microenv/cci/__init__.py
stlearn/tools/microenv/cci/base.py
stlearn/tools/microenv/cci/het.py
stlearn/tools/microenv/cci/merge.py
stlearn/tools/microenv/cci/permutation.py
stlearn/wrapper/__init__.py
stlearn/wrapper/convert_scanpy.py
stlearn/wrapper/read.py
tests/__init__.py
tests/test_CCI.py
tests/test_PSTS.py
tests/test_SME.py
tests/utils.py
tests/test_data/test_data.h5
tests/test_data/test_image.jpg
tutorials/README.md
tutorials/connectomedb2020.txt
tutorials/label_transfer_bc.csv
tutorials/means.txt
tutorials/predictions.csv