├── LICENSE ├── README.md ├── Snakefile ├── envs ├── env.yml ├── env_bbknn.yml ├── env_bus.yml ├── env_combatseq.yml ├── env_down.yml ├── env_harmony.yml ├── env_liger.yml ├── env_mast.yml ├── env_mnn.yml ├── env_scvi.yml ├── env_scvi_new.yml ├── env_seurat.yml └── env_test.yml └── scripts ├── batch_report.py ├── create_output.py ├── create_output_diffexp.py ├── diffexp_report.py ├── export_batch_plot.py ├── extra_plots.R ├── methods.py ├── mod_base.py ├── mod_base_heart.py ├── mod_base_jejunum.py ├── mod_base_neuro.py ├── mod_base_pbmc4k.py ├── mod_bbknn.py ├── mod_combat.py ├── mod_combatseq.R ├── mod_combatseq.py ├── mod_down.py ├── mod_harmony.R ├── mod_harmony.py ├── mod_heart.py ├── mod_mast.R ├── mod_mnn.R ├── mod_mnn.py ├── mod_pyliger.py ├── mod_pyliger_v2.py ├── mod_resample.py ├── mod_scvi.py ├── mod_seurat.R ├── mod_seurat.py ├── mod_seurat_v2.py ├── mod_simulated.py ├── plot_results.R ├── supplemental_analysis.R └── supplemental_analysis.py /LICENSE: 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