├── .DS_Store ├── LICENSE ├── R process ├── ATAC │ ├── PBMC_Signac_ATAC.R │ └── mouse_spleen_ATAC.R ├── CITE │ └── BM_CITE.R ├── HPRI │ └── MERFISH.R └── spot │ ├── BRCA_SPOT.R │ ├── Brain_SPOT.R │ ├── GSE111672_PDAC-A-indrop-filtered-expMat.txt.gz │ ├── GSM3036911_PDAC-A-ST1-filtered.txt.gz │ ├── PDAC_SPOT.R │ └── spatial_function.R ├── README.md ├── __init__.py ├── docs ├── .DS_Store ├── Makefile ├── make.bat └── source │ ├── .DS_Store │ ├── API │ ├── .ipynb_checkpoints │ │ ├── Run-checkpoint.ipynb │ │ └── load_file-checkpoint.ipynb │ ├── index.rst │ ├── uniport.Run.rst │ ├── uniport.batch_scale.rst │ ├── uniport.data_loader.BatchSampler.rst │ ├── uniport.data_loader.BatchSampler_balance.rst │ ├── uniport.data_loader.SingleCellDataset.rst │ ├── uniport.data_loader.SingleCellDataset_vertical.rst │ ├── uniport.data_loader.load_data.rst │ ├── uniport.filter_data.rst │ ├── uniport.label_reweight.rst │ ├── uniport.load_file.rst │ ├── uniport.logger.create_logger.rst │ ├── uniport.metrics.batch_entropy_mixing_score.rst │ ├── uniport.metrics.label_transfer.rst │ ├── uniport.metrics.silhouette.rst │ ├── uniport.model.layer.Block.rst │ ├── uniport.model.layer.DSBatchNorm.rst │ ├── uniport.model.layer.Decoder.rst │ ├── uniport.model.layer.Encoder.rst │ ├── uniport.model.layer.NN.rst │ ├── uniport.model.loss.distance_gmm.rst │ ├── uniport.model.loss.distance_matrix.rst │ ├── uniport.model.loss.kl_div.rst │ ├── uniport.model.loss.unbalanced_ot.rst │ ├── uniport.model.utils.EarlyStopping.rst │ ├── uniport.model.utils.onehot.rst │ └── uniport.model.vae.VAE.rst │ ├── README.md │ ├── _static │ ├── net.png │ ├── uniPort.jpg │ └── uniPort.png │ ├── _templates │ ├── README.md │ ├── class.rst │ └── module.rst │ ├── conf.py │ ├── examples │ ├── .DS_Store │ ├── .ipynb_checkpoints │ │ ├── pbmc_integration-checkpoint.ipynb │ │ ├── pbmc_preprocess-checkpoint.ipynb │ │ └── vertical_snare_cell_line-checkpoint.ipynb │ ├── BRCA │ │ ├── BRCA.ipynb │ │ ├── BRCA_CAFs_Cancer.Epithelial.png │ │ ├── BRCA_celltype_LT_T_i60k_md.png │ │ ├── BRCA_plot.rst │ │ └── brca.rst │ ├── MERFISH │ │ ├── .ipynb_checkpoints │ │ │ ├── MERFISH_predict-checkpoint.ipynb │ │ │ └── MERFISH_preprocess-checkpoint.ipynb │ │ ├── MERFISH_and_scRNA.ipynb │ │ ├── MERFISH_impute.ipynb │ │ ├── MERFISH_predict.ipynb │ │ └── merfish.rst │ ├── PBMC │ │ ├── .DS_Store │ │ ├── .ipynb_checkpoints │ │ │ ├── mouse_spleen-checkpoint.ipynb │ │ │ ├── pbmc_integration-checkpoint.ipynb │ │ │ └── pbmc_preprocess-checkpoint.ipynb │ │ ├── mouse_spleen.ipynb │ │ ├── pbmc.rst │ │ └── pbmc_integration.ipynb │ ├── PDAC │ │ ├── OT_PDAC_LF_F.png │ │ ├── PDAC_CA_Ductal.png │ │ ├── PDAC_integration.ipynb │ │ ├── PDAC_plot.rst │ │ └── pdac.rst │ ├── diagonal_PBMC.ipynb │ ├── index.rst │ └── vertical_snare_cell_line.ipynb │ ├── index.rst │ ├── install.rst │ └── release.rst ├── pyproject.toml ├── requirements.txt └── uniport ├── .DS_Store ├── LICENSE.txt ├── __init__.py ├── data_loader.py ├── 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