.gitignore
CHANGELOG.md
LICENSE
README.md
pyproject.toml
ONTraC/__init__.py
ONTraC/data.py
ONTraC/log.py
ONTraC/version.py
ONTraC.egg-info/PKG-INFO
ONTraC.egg-info/SOURCES.txt
ONTraC.egg-info/dependency_links.txt
ONTraC.egg-info/entry_points.txt
ONTraC.egg-info/requires.txt
ONTraC.egg-info/top_level.txt
ONTraC/__pycache__/__init__.cpython-311.pyc
ONTraC/__pycache__/__init__.cpython-312.pyc
ONTraC/bin/GP.py
ONTraC/bin/NTScore.py
ONTraC/bin/ONTraC.py
ONTraC/bin/__init__.py
ONTraC/bin/createDataSet.py
ONTraC/model/__init__.py
ONTraC/model/_model.py
ONTraC/model/dmon_exp_pool.py
ONTraC/model/norm_dense_gcn_conv.py
ONTraC/optparser/_GP.py
ONTraC/optparser/_IO.py
ONTraC/optparser/_NT.py
ONTraC/optparser/_ONTraC.py
ONTraC/optparser/__init__.py
ONTraC/optparser/_create_dataset.py
ONTraC/optparser/_train.py
ONTraC/run/processes.py
ONTraC/train/__init__.py
ONTraC/train/_batch_train.py
ONTraC/train/inspect_funcs.py
ONTraC/train/loss_funs.py
ONTraC/utils/NTScore.py
ONTraC/utils/__init__.py
ONTraC/utils/_utils.py
ONTraC/utils/decorators.py
ONTraC/utils/niche_net_constr.py
ONTraC/utils/__pycache__/__init__.cpython-311.pyc
ONTraC/utils/__pycache__/__init__.cpython-312.pyc
ONTraC/utils/__pycache__/_utils.cpython-311.pyc
ONTraC/utils/__pycache__/_utils.cpython-312.pyc
docs/source/_static/images/ONTraC_structure.png
docs/source/_static/images/examples/simulation/simulation_dataset_introduction.png
docs/source/_static/images/tutorials/niche_cluster/Spatial_niche_cluster.png
docs/source/_static/images/tutorials/niche_cluster/spatial_cluster_prob_E14.png
docs/source/_static/images/tutorials/post_analysis/Spatial_cell_type.png
docs/source/_static/images/tutorials/post_analysis/cell_level_NT_score.png
docs/source/_static/images/tutorials/post_analysis/cell_level_NT_score_distribution_for_each_cell_type.png
docs/source/_static/images/tutorials/post_analysis/cell_type_compostion.png
docs/source/_static/images/tutorials/post_analysis/niche_level_NT_score.png
examples/simulation/README.md
examples/simulation/original_data.csv
examples/simulation/pseudotime_output.csv
examples/simulation/simulation_dataset_sce.rds
examples/stereo_seq_brain/Stereo_seq_example.md
examples/stereo_seq_brain/original_data.csv
examples/stereo_seq_brain/stereo_seq_final.log
examples/stereo_seq_brain/stereo_seq_final_GNN/E12_E1S3_out.csv.gz
examples/stereo_seq_brain/stereo_seq_final_GNN/E12_E1S3_out_adj.csv.gz
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examples/stereo_seq_brain/stereo_seq_final_GNN/consolidate_s.csv.gz
examples/stereo_seq_brain/stereo_seq_final_GNN/epoch_0.pt
examples/stereo_seq_brain/stereo_seq_final_GNN/model_state_dict.pt
examples/stereo_seq_brain/stereo_seq_final_NTScore/E12_E1S3_NTScore.csv.gz
examples/stereo_seq_brain/stereo_seq_final_NTScore/E14_E1S3_NTScore.csv.gz
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examples/stereo_seq_brain/stereo_seq_final_NTScore/niche_cluster_score.csv.gz
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examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E1S3_NicheWeightMatrix.npz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S6_CellTypeComposition.csv.gz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S6_Coordinates.csv
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examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S6_NeighborIndicesMatrix.csv.gz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S6_NicheWeightMatrix.npz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S7_CellTypeComposition.csv.gz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S7_Coordinates.csv
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examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S7_NeighborIndicesMatrix.csv.gz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/E16_E2S7_NicheWeightMatrix.npz
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/cell_type_code.csv
examples/stereo_seq_brain/stereo_seq_final_preprocessing_dir/samples.yaml
tutorials/IO_files.md
tutorials/niche_cluster.md
tutorials/post_analysis.md