.gitignore
.readthedocs.yml
LICENSE
README.md
pyproject.toml
quick_start.ipynb
requirements.txt
requirements_for_image.txt
requirements_for_spatialign.txt
setup.py
.github/workflows/main.yml
.github/workflows/pytest_conda_linux.yml
.github/workflows/pytest_conda_linux_dev.yml
.github/workflows/pytest_conda_linux_gpu.yml
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stereo/__init__.py
stereo/common.py
stereo/constant.py
stereo/log_manager.py
stereo/stereo_config.py
stereo/algorithm/__init__.py
stereo/algorithm/_louvain.py
stereo/algorithm/algorithm_base.py
stereo/algorithm/algorithm_err_code.py
stereo/algorithm/cell_correction.py
stereo/algorithm/cell_correction_fast.py
stereo/algorithm/cell_correction_fast_by_mask.py
stereo/algorithm/co_occurrence.py
stereo/algorithm/community_detection.py
stereo/algorithm/dendrogram.py
stereo/algorithm/dim_reduce.py
stereo/algorithm/draw_contours.py
stereo/algorithm/gaussian_smooth.py
stereo/algorithm/gen_ccc_micro_envs.py
stereo/algorithm/gen_mesh.py
stereo/algorithm/get_niche.py
stereo/algorithm/highly_variable_genes.py
stereo/algorithm/leiden.py
stereo/algorithm/log1p_fake.py
stereo/algorithm/mannwhitneyu.py
stereo/algorithm/ms_algorithm_base.py
stereo/algorithm/ms_community_detection.py
stereo/algorithm/ms_log1p_fake.py
stereo/algorithm/neighbors.py
stereo/algorithm/normalization.py
stereo/algorithm/paga.py
stereo/algorithm/phenograph.py
stereo/algorithm/scale.py
stereo/algorithm/scenic.py
stereo/algorithm/spatial_hotspot.py
stereo/algorithm/spatial_pattern_score.py
stereo/algorithm/statistics.py
stereo/algorithm/time_series_analysis.py
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stereo/algorithm/umap.py
stereo/algorithm/batch_qc/__init__.py
stereo/algorithm/batch_qc/batchqc_raw.py
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stereo/algorithm/batch_qc/module/trainer.py
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stereo/algorithm/batch_qc/score/lisi.py
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stereo/algorithm/batch_qc/test/cdf_plot.py
stereo/algorithm/batch_qc/test/describe_data.py
stereo/algorithm/batch_qc/test/distribution_fitting.py
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stereo/algorithm/batch_qc/test/umap_plot.py
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stereo/algorithm/batch_qc/test/variance_test.py
stereo/algorithm/batch_qc/utils/__init__.py
stereo/algorithm/batch_qc/utils/check_data.py
stereo/algorithm/batch_qc/utils/generate_palette.py
stereo/algorithm/batch_qc/utils/html_utils.py
stereo/algorithm/batch_qc/utils/pca_lowrank.py
stereo/algorithm/batch_qc/utils/print_time.py
stereo/algorithm/ccd/__init__.py
stereo/algorithm/ccd/community_clustering_algorithm.py
stereo/algorithm/ccd/constants.py
stereo/algorithm/ccd/html_report.py
stereo/algorithm/ccd/metrics.py
stereo/algorithm/ccd/sliding_window.py
stereo/algorithm/ccd/utils.py
stereo/algorithm/ccd/assets/favicon.ico
stereo/algorithm/cell_cell_communication/__init__.py
stereo/algorithm/cell_cell_communication/analysis_helper.py
stereo/algorithm/cell_cell_communication/exceptions.py
stereo/algorithm/cell_cell_communication/main.py
stereo/algorithm/cell_cell_communication/plot_ccc.py
stereo/algorithm/cell_cell_communication/spatial_scoloc.py
stereo/algorithm/cell_cell_communication/utils/__init__.py
stereo/algorithm/cell_cell_communication/utils/database_utils.py
stereo/algorithm/cell_cell_communication/utils/sqlalchemy_model.py
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stereo/algorithm/cell_cell_communication/utils/visualization_process.py
stereo/algorithm/cell_pose/__init__.py
stereo/algorithm/cell_pose/cell_pose.py
stereo/algorithm/cell_pose/core.py
stereo/algorithm/cell_pose/dynamics.py
stereo/algorithm/cell_pose/io.py
stereo/algorithm/cell_pose/metrics.py
stereo/algorithm/cell_pose/models.py
stereo/algorithm/cell_pose/plot.py
stereo/algorithm/cell_pose/resnet_torch.py
stereo/algorithm/cell_pose/utils.py
stereo/algorithm/cell_pose/version.py
stereo/algorithm/dpt/__init__.py
stereo/algorithm/dpt/main.py
stereo/algorithm/dpt/pca.py
stereo/algorithm/dpt/struct.py
stereo/algorithm/paste/__init__.py
stereo/algorithm/paste/helper.py
stereo/algorithm/paste/methods.py
stereo/algorithm/paste/paste.py
stereo/algorithm/regulatory_network_inference/__init__.py
stereo/algorithm/regulatory_network_inference/main.py
stereo/algorithm/regulatory_network_inference/plot_grn.py
stereo/algorithm/sctransform/__init__.py
stereo/algorithm/sctransform/bw.py
stereo/algorithm/sctransform/ksmooth.py
stereo/algorithm/sctransform/plotting.py
stereo/algorithm/sctransform/scale_data.py
stereo/algorithm/sctransform/sctransform.py
stereo/algorithm/sctransform/utils.py
stereo/algorithm/sctransform/vst.py
stereo/algorithm/single_r/__init__.py
stereo/algorithm/single_r/single_r.py
stereo/algorithm/single_r/utils.py
stereo/core/__init__.py
stereo/core/cell.py
stereo/core/constants.py
stereo/core/data.py
stereo/core/gene.py
stereo/core/ms_data.py
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stereo/core/result.py
stereo/core/st_pipeline.py
stereo/core/stereo_exp_data.py
stereo/core/tool_base.py
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stereo/data/algorithm/cell_cell_communication/database/celltalkdb.db
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stereo/image/__init__.py
stereo/image/pyramid.py
stereo/image/segmentation/__init__.py
stereo/image/segmentation/segment.py
stereo/image/segmentation/seg_utils/base_cell_seg_pipe/__init__.py
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stereo/image/segmentation/seg_utils/v1/models/__init__.py
stereo/image/segmentation/seg_utils/v1/models/epsanet.py
stereo/image/segmentation/seg_utils/v1_pro/__init__.py
stereo/image/segmentation/seg_utils/v1_pro/cell_infer.py
stereo/image/segmentation/seg_utils/v1_pro/cell_seg_pipeline_v1_pro.py
stereo/image/segmentation/seg_utils/v1_pro/dataset.py
stereo/image/segmentation/seg_utils/v1_pro/find_maxima.py
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stereo/image/segmentation/seg_utils/v1_pro/image.py
stereo/image/segmentation/seg_utils/v1_pro/resnet_unet.py
stereo/image/segmentation/seg_utils/v1_pro/tissue_seg.py
stereo/image/segmentation/seg_utils/v1_pro/tissue_seg_pipeline.py
stereo/image/segmentation/seg_utils/v1_pro/utils.py
stereo/image/segmentation/seg_utils/v1_pro/models/SE_weight_module.py
stereo/image/segmentation/seg_utils/v1_pro/models/__init__.py
stereo/image/segmentation/seg_utils/v1_pro/models/epsanet.py
stereo/image/segmentation/seg_utils/v3/__init__.py
stereo/image/segmentation/seg_utils/v3/cell_seg_pipeline_v3.py
stereo/image/segmentation_deepcell/__init__.py
stereo/image/segmentation_deepcell/segment.py
stereo/image/segmentation_deepcell/seg_utils/__init__.py
stereo/image/segmentation_deepcell/seg_utils/cell_infer.py
stereo/image/segmentation_deepcell/seg_utils/cell_seg_pipeline.py
stereo/image/segmentation_deepcell/seg_utils/find_maxima.py
stereo/image/segmentation_deepcell/seg_utils/grade.py
stereo/image/segmentation_deepcell/seg_utils/image.py
stereo/image/segmentation_deepcell/seg_utils/tissue_seg.py
stereo/image/segmentation_deepcell/seg_utils/tissue_seg_pipeline.py
stereo/image/segmentation_deepcell/seg_utils/utils.py
stereo/image/tissue_cut/__init__.py
stereo/image/tissue_cut/pipeline.py
stereo/image/tissue_cut/tissue_cut_utils/__init__.py
stereo/image/tissue_cut/tissue_cut_utils/tissue_seg_bcdu.py
stereo/image/tissue_cut/tissue_cut_utils/tissue_seg_bcdu_model.py
stereo/image/tissue_cut/tissue_cut_utils/tissue_seg_bcdu_uity.py
stereo/image/tissue_cut/tissue_cut_utils/tissue_seg_net.py
stereo/image/tissue_cut/tissue_cut_utils/tissue_seg_utils.py
stereo/image/x2tif/__init__.py
stereo/image/x2tif/x2tif.py
stereo/io/__init__.py
stereo/io/h5ad.py
stereo/io/reader.py
stereo/io/writer.py
stereo/plots/__init__.py
stereo/plots/decorator.py
stereo/plots/marker_genes.py
stereo/plots/ms_plot.py
stereo/plots/ms_plot_base.py
stereo/plots/plot_base.py
stereo/plots/plot_ccd.py
stereo/plots/plot_cells.py
stereo/plots/plot_clusters_heatmap.py
stereo/plots/plot_clusters_scatter.py
stereo/plots/plot_collection.py
stereo/plots/plot_coo.py
stereo/plots/plot_dendrogram.py
stereo/plots/plot_elbow.py
stereo/plots/plot_genes_in_pseudotime.py
stereo/plots/plot_paga.py
stereo/plots/plot_time_series.py
stereo/plots/scatter.py
stereo/plots/test
stereo/plots/violin.py
stereo/plots/_plot_basic/__init__.py
stereo/plots/_plot_basic/get_stereo_data.py
stereo/plots/_plot_basic/heatmap_plt.py
stereo/plots/interact_plot/__init__.py
stereo/plots/interact_plot/annotation_cluster.py
stereo/plots/interact_plot/interactive_scatter.py
stereo/plots/interact_plot/poly_selection.py
stereo/plots/interact_plot/spatial_cluster.py
stereo/plots/plot_cluster_traj/__init__.py
stereo/plots/plot_cluster_traj/interp.py
stereo/plots/plot_cluster_traj/plot_cluster_traj.py
stereo/plots/plot_cluster_traj/traj.py
stereo/plots/plot_cluster_traj_3d/__init__.py
stereo/plots/plot_cluster_traj_3d/interp.py
stereo/plots/plot_cluster_traj_3d/plot_cluster_traj_3d.py
stereo/plots/plot_cluster_traj_3d/traj.py
stereo/plots/plot_vec/__init__.py
stereo/plots/plot_vec/plot_vec.py
stereo/plots/plot_vec/vec.py
stereo/plots/plot_vec_3d/__init__.py
stereo/plots/plot_vec_3d/plot_vec_3d.py
stereo/plots/plot_vec_3d/vec.py
stereo/plots/vt3d_browser/PAGA_traj.py
stereo/plots/vt3d_browser/README.md
stereo/plots/vt3d_browser/__init__.py
stereo/plots/vt3d_browser/example.py
stereo/plots/vt3d_browser/stereopy_3D_browser.py
stereo/plots/vt3d_browser/examples/example_ccc.ipynb
stereo/plots/vt3d_browser/examples/example_grn.ipynb
stereo/plots/vt3d_browser/examples/example_mesh.ipynb
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stereo/preprocess/__init__.py
stereo/preprocess/filter.py
stereo/preprocess/normalize.py
stereo/preprocess/qc.py
stereo/preprocess/sc_transform.py
stereo/scripts/__init__.py
stereo/scripts/ccd.py
stereo/tools/LR_interaction.py
stereo/tools/__init__.py
stereo/tools/boundary.py
stereo/tools/cell_correct.py
stereo/tools/cell_cut.py
stereo/tools/cell_segment.py
stereo/tools/cell_type_anno.py
stereo/tools/cluster.py
stereo/tools/clustering.py
stereo/tools/dim_reduce.py
stereo/tools/find_markers.py
stereo/tools/gem_filter.py
stereo/tools/highly_variable_genes.py
stereo/tools/rna_velocity.py
stereo/tools/spatial_lag.py
stereo/tools/spatial_pattern_score.py
stereo/tools/tissue_extraction.py
stereo/tools/tools.py
stereo/utils/__init__.py
stereo/utils/_download.py
stereo/utils/correlation.py
stereo/utils/data_helper.py
stereo/utils/hvg_utils.py
stereo/utils/pipeline_utils.py
stereo/utils/read_write_utils.py
stereo/utils/spmatrix_helper.py
stereo/utils/time_consume.py
stereopy.egg-info/PKG-INFO
stereopy.egg-info/SOURCES.txt
stereopy.egg-info/dependency_links.txt
stereopy.egg-info/entry_points.txt
stereopy.egg-info/requires.txt
stereopy.egg-info/top_level.txt
tests/extra_requirements.txt
tests/image_requirements.txt
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tests/test_batch_integration.py
tests/test_cell_community_detection.py
tests/test_cell_cut.py
tests/test_clustering.py
tests/test_h5ad_format.py
tests/test_io.py
tests/test_io_h5ms.py
tests/test_marker_genes.py
tests/test_merge_3d_data.py
tests/test_ms_data.py
tests/test_plot_cluster_traj.py
tests/test_plot_vec.py
tests/test_regulatory_network_inference.py
tests/test_rna_velocity.py
tests/test_sctransform.py
tests/test_single_r.py
tests/test_spatial_hotspot.py
tests/test_stereo_exp_data.py
tests/test_time_series_analysis.py
tests/workflows_conf/environment_linux_gpu.yml
tests/workflows_conf/environment_linux_py38.yml
tests/workflows_conf/environment_linux_py39.yml
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