├── .gitignore ├── CLEAR.py ├── README.md ├── compared_methods ├── CIDR │ ├── CIDR_dropout.R │ ├── CIDR_dropout_facs.R │ └── run_CIDR.r ├── ItClust-train.py ├── README.md ├── SC3 │ ├── SC3_dropout.R │ ├── SC3_dropout_facs.R │ └── run_SC3.r ├── SIMLR │ ├── SIMLR-train-large-scale.R │ ├── SIMLR-train.R │ └── train_SIMLR-backup.R ├── SINCERA │ ├── SINCERA_dropout.R │ ├── SINCERA_dropout_facs.R │ └── run_SINCERA.r ├── Seurat │ ├── Seurat_dropout.R │ ├── Seurat_dropout_facs.R │ ├── batch_seurat.R │ └── run_Seurat.R ├── direct-kmeans.py ├── scDHA-train.R ├── scGNN │ ├── .gitignore │ ├── LICENCE │ ├── LTMG_R.py │ ├── Preprocessing_benchmark.py │ ├── Preprocessing_main.py │ ├── PreprocessingscGNN.py │ ├── README.md │ ├── benchmark_util.py │ ├── clustering_metric.py │ ├── gae │ │ ├── layers.py │ │ ├── model.py │ │ ├── optimizer.py │ │ ├── train.py │ │ └── utils.py │ ├── gae_embedding.py │ ├── graph_function.py │ ├── main_benchmark.py │ ├── model.py │ ├── reproduce │ │ └── REPRODUCIBILITY.md │ ├── requirements.txt │ ├── scGNN-cluster.py │ ├── scGNN.py │ ├── tutorial │ │ └── Tutorial.md │ └── util_function.py └── scVI-train.py ├── data ├── README.md └── data-download.sh ├── environment.yml ├── illustrations ├── fig2 │ └── README.md ├── fig3 │ └── README.md ├── fig4 │ └── README.md ├── fig5 │ ├── Fig5.Peripheral_immune_cells_atlas_and_inflammatory-related_mechanisms_in_COVID-19_revealed_by_CLEAR.Rmd │ └── README.md └── fig6 │ └── README.md ├── metrics.py ├── pcl ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── builder.cpython-38.pyc │ └── loader.cpython-38.pyc ├── builder.py └── loader.py ├── preprocess ├── README.md ├── SCTransform.py ├── __pycache__ │ └── SCTransform.cpython-38.pyc ├── data │ └── pbmc3k_raw.h5ad ├── generate_h5ad.py ├── rds_to_csv.R └── test │ ├── pbmc3k_raw_preprocessed.h5ad │ └── pbmc3k_raw_sct.h5ad ├── reproduce └── batch_effect └── result └── CLEAR ├── feature_CLEAR_pbmc3k_raw_preprocessed.csv └── log_CLEAR_pbmc3k_raw_preprocessed.txt 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