.gitignore
.readthedocs.yml
LICENSE
README.md
requirements.txt
setup.py
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/roadmap.md
docs/stereo_frame_v0.2.md
docs/source/conf.py
docs/source/index.rst
docs/source/release_note.rst
docs/source/General/Installation.rst
docs/source/Tutorials/Examples.rst
docs/source/Tutorials/interactive_cluster.ipynb
docs/source/Tutorials/quick_start.ipynb
docs/source/Tutorials/quick_start_v0.1.ipynb
docs/source/_static/degs.png
docs/source/_static/heatmap.png
docs/source/_static/html.css
docs/source/_static/schema.png
docs/source/_static/spatial_cluster.png
docs/source/_static/spatial_distribution.png
docs/source/_static/stereopy.PNG
docs/source/_static/violin_distribution.png
docs/source/api/index.rst
stereo/__init__.py
stereo/config.py
stereo/log_manager.py
stereo/algorithm/__init__.py
stereo/algorithm/_louvain.py
stereo/algorithm/dim_reduce.py
stereo/algorithm/highly_variable_genes.py
stereo/algorithm/leiden.py
stereo/algorithm/neighbors.py
stereo/algorithm/normalization.py
stereo/algorithm/phenograph.py
stereo/algorithm/spatial_pattern_score.py
stereo/algorithm/statistics.py
stereo/algorithm/umap.py
stereo/algorithm/pysctransform/__init__.py
stereo/algorithm/pysctransform/fit.py
stereo/algorithm/pysctransform/fit_glmgp.py
stereo/algorithm/pysctransform/jax_bfgs.py
stereo/algorithm/pysctransform/plotting.py
stereo/algorithm/pysctransform/pysctransform.py
stereo/algorithm/pysctransform/r_bw.py
stereo/core/__init__.py
stereo/core/cell.py
stereo/core/data.py
stereo/core/gene.py
stereo/core/st_pipeline.py
stereo/core/stereo_exp_data.py
stereo/core/stereo_result.py
stereo/core/tool_base.py
stereo/image/__init__.py
stereo/image/pyramid.py
stereo/image/segmentation/__init__.py
stereo/image/segmentation/segment.py
stereo/image/segmentation/seg_utils/__init__.py
stereo/image/segmentation/seg_utils/cell_infer.py
stereo/image/segmentation/seg_utils/cell_seg_pipeline.py
stereo/image/segmentation/seg_utils/find_maxima.py
stereo/image/segmentation/seg_utils/grade.py
stereo/image/segmentation/seg_utils/image.py
stereo/image/segmentation/seg_utils/tissue_seg.py
stereo/image/segmentation/seg_utils/tissue_seg_pipeline.py
stereo/image/segmentation/seg_utils/utils.py
stereo/io/__init__.py
stereo/io/gef.py
stereo/io/h5ad.py
stereo/io/reader.py
stereo/io/writer.py
stereo/plots/__init__.py
stereo/plots/marker_genes.py
stereo/plots/plot_collection.py
stereo/plots/qc.py
stereo/plots/scatter.py
stereo/plots/_plot_basic/__init__.py
stereo/plots/_plot_basic/get_stereo_data.py
stereo/plots/_plot_basic/heatmap_plt.py
stereo/plots/_plot_basic/scatter_plt.py
stereo/plots/interact_plot/__init__.py
stereo/plots/interact_plot/interactive_scatter.py
stereo/plots/interact_plot/spatial_cluster.py
stereo/preprocess/__init__.py
stereo/preprocess/filter.py
stereo/preprocess/normalize.py
stereo/preprocess/qc.py
stereo/preprocess/sc_transform.py
stereo/tools/__init__.py
stereo/tools/cell_type_anno.py
stereo/tools/cluster.py
stereo/tools/cluster_new.py
stereo/tools/clustering.py
stereo/tools/dim_reduce.py
stereo/tools/find_markers.py
stereo/tools/highly_variable_genes.py
stereo/tools/spatial_lag.py
stereo/tools/spatial_pattern_score.py
stereo/utils/__init__.py
stereo/utils/correlation.py
stereo/utils/data_helper.py
stereo/utils/hvg_utils.py
stereo/utils/spmatrix_helper.py
stereopy.egg-info/PKG-INFO
stereopy.egg-info/SOURCES.txt
stereopy.egg-info/dependency_links.txt
stereopy.egg-info/requires.txt
stereopy.egg-info/top_level.txt
tests/data_parse.py
tests/test_cell_type_anno.py
tests/test_clustering.py
tests/test_data_helper.py
tests/test_dim_reduce.py
tests/test_filter.py
tests/test_find_markers.py
tests/test_gsea.py
tests/test_hvgs.py
tests/test_image_pyramid.py
tests/test_interactive_scatter.py
tests/test_normalize.py
tests/test_plots.py
tests/test_qc.py
tests/test_reader.py
tests/test_sc_transform.py
tests/test_sc_transfrom.ipynb
tests/test_segment.py
tests/test_spatial_lag.py
tests/test_spatial_pattern.py
tests/test_stereo_exp_data.py
tests/test_tools.py
tests/test_writer.py