.gitignore
.readthedocs.yml
AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
Makefile
README.md
requirements.txt
requirements_dev.txt
setup.cfg
setup.py
tox.ini
stlearn/__init__.py
stlearn/__main__.py
stlearn/_compat.py
stlearn/_settings.py
stlearn/add.py
stlearn/cli.py
stlearn/em.py
stlearn/gui.py
stlearn/logging.py
stlearn/pl.py
stlearn/pp.py
stlearn/read.py
stlearn/spatial.py
stlearn/tl.py
stlearn/utils.py
stlearn/view.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/adds/__init__.py
stlearn/adds/add_cpdb.py
stlearn/adds/add_image.py
stlearn/adds/add_lr.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/cci_plot.py
stlearn/plotting/cluster_plot.py
stlearn/plotting/enrichment_analysis_plot.py
stlearn/plotting/gene_plot.py
stlearn/plotting/microenv_plot.py
stlearn/plotting/non_spatial_plot.py
stlearn/plotting/subcluster_plot.py
stlearn/plotting/utils.py
stlearn/plotting/trajectory/__init__.py
stlearn/plotting/trajectory/local_plot.py
stlearn/plotting/trajectory/pseudotime_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/reads/__init__.py
stlearn/reads/read.py
stlearn/spatials/__init__.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/global_level.py
stlearn/spatials/trajectory/local_level.py
stlearn/spatials/trajectory/pseudotime.py
stlearn/tools/__init__.py
stlearn/tools/clustering/__init__.py
stlearn/tools/clustering/kmeans.py
stlearn/tools/clustering/louvain.py
stlearn/tools/enrichment_analysis/__init__.py
stlearn/tools/enrichment_analysis/enrichr.py
stlearn/tools/enrichment_analysis/microenv.py
stlearn/tools/microenv/__init__.py
stlearn/tools/microenv/SpatialDE/aeh.py
stlearn/tools/microenv/SpatialDE/aha.py
stlearn/tools/microenv/SpatialDE/anndata.py
stlearn/tools/microenv/SpatialDE/base.py
stlearn/tools/microenv/SpatialDE/plot.py
stlearn/tools/microenv/SpatialDE/util.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/views/__init__.py
stlearn/views/microenv_view.py
stlearn/views/pts_view.py
stlearn/wrapper/__init__.py
stlearn/wrapper/clustering.py
stlearn/wrapper/preprocessing.py
stlearn/wrapper/pts.py
stlearn/wrapper/read.py
tests/__init__.py
tests/test_stlearn.py
tutorials/Pseudo-space-time-tutorial.ipynb
tutorials/README.md
tutorials/Read_MERFISH.ipynb
tutorials/Read_slideseq.ipynb
tutorials/Working-with-Old-Spatial-Transcriptomics-data.ipynb
tutorials/cci.ipynb
tutorials/predictions.csv
tutorials/spatialDE.ipynb
tutorials/stSME_clustering.ipynb