├── .DS_Store ├── .idea ├── HarmonizationSCANVI.iml ├── deployment.xml ├── dictionaries │ └── chenlingantelope.xml ├── inspectionProfiles │ └── Project_Default.xml ├── libraries │ └── R_User_Library.xml ├── misc.xml ├── modules.xml ├── other.xml ├── remote-mappings.xml ├── vcs.xml └── workspace.xml ├── AUTHORS.rst ├── Additional_Scripts ├── .DS_Store ├── BE_curves.py ├── CD4BCELL.DN.gmt ├── CD4BCELL.UP.gmt ├── CD4CD8.DN.gmt ├── CD4CD8.UP.gmt ├── CD8BCELL.DN.gmt ├── CD8BCELL.UP.gmt ├── CD8NK.DN.gmt ├── CD8NK.UP.gmt ├── GrepGeneSignatures.sh ├── KNNcurves.py ├── NoOverlapboxplot.R ├── PopRemoveboxplot.R ├── SeuratPCA.R ├── Seurat_hvginfo.R ├── UniquePopsboxplot.R ├── c7.all.v6.2.symbols.gmt ├── genesets.txt ├── prep_gbm.R ├── runEdgeR.PBMC.R ├── runEdgeR.R ├── runSeurat.R ├── scanvi_acc.R └── test.py ├── CONTRIBUTING.rst ├── DentateGyrus.py ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── MarrowTM.py ├── NoOverlapSCANVI.py ├── PBMC8KCITE.py ├── Pancreas.py ├── PopRemoveSCANVI.py ├── README.md ├── README.rst ├── UniquePopsSCANVI.py ├── cluster_acc.py ├── data └── gene_len.txt ├── de_PBMC2.py ├── de_simulations.py ├── de_simulations2.py ├── docs ├── .DS_Store ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── make.bat ├── readme.rst ├── requirements.txt ├── scvi.dataset.rst ├── scvi.inference.rst ├── scvi.models.rst └── scvi.rst ├── evalEdgeR.py ├── notebooks ├── .DS_Store ├── .gitignore ├── .ipynb_checkpoints │ ├── BICCN_data-Macosko_Regev-checkpoint.ipynb │ ├── BICCN_data-checkpoint.ipynb │ ├── CBMC_PBMC-checkpoint.ipynb │ ├── CSF-MichaelData-checkpoint.ipynb │ ├── CSF-checkpoint.ipynb │ ├── DE-final-Copy1-checkpoint.ipynb │ ├── DE-final-checkpoint.ipynb │ ├── DentateGyrus-checkpoint.ipynb │ ├── Hierarchical-Copy1-checkpoint.ipynb │ ├── Hierarchical-checkpoint.ipynb │ ├── Macosko_Hierarchy-checkpoint.ipynb │ ├── Marketing-checkpoint.ipynb │ ├── Pancreas_check-checkpoint.ipynb │ ├── SCANVI-mild-annot-Clustering-checkpoint.ipynb │ ├── SCANVI-mild-annot-Copy2-checkpoint.ipynb │ ├── SCANVI-mild-annot-checkpoint.ipynb │ ├── SCANVI-robustness-checkpoint.ipynb │ ├── SCANVI_paramsearch-Copy1-checkpoint.ipynb │ ├── SCANVI_posterior-Copy1-checkpoint.ipynb │ ├── SCANVI_posterior-NoOverlap-checkpoint.ipynb │ ├── SCANVI_posterior_poprm-checkpoint.ipynb │ ├── Tech1.pretty-checkpoint.ipynb │ ├── Tech3.pretty-checkpoint.ipynb │ ├── continuous-checkpoint.ipynb │ ├── harmonization-CitePure-SCANVI-checkpoint.ipynb │ ├── harmonization-CitePure-checkpoint.ipynb │ ├── harmonization-checkpoint.ipynb │ └── scanorama-checkpoint.ipynb ├── ContinuousSymSim.ipynb ├── DE-final.ipynb ├── DE_simulation-mislabelled.ipynb ├── DE_simulation-nb.ipynb ├── DE_simulation.ipynb ├── DE_umap.ipynb ├── Hierarchical-final.ipynb ├── Magan.ipynb ├── MarrowTM_connectivity.ipynb ├── Nclasses.ipynb ├── PBMC_DE.ipynb ├── Robustness_study.ipynb ├── SCANVI-mild-annot-Clustering.ipynb ├── Tech1.pretty.ipynb ├── continuous.ipynb ├── harmonization-CitePure-SCANVI.ipynb ├── prior_l-TM.ipynb ├── prior_l.ipynb ├── runtime.ipynb └── scanorama.ipynb ├── read_results_DE.py ├── readthedocs.yml ├── requirements.txt ├── scanorama.py ├── scanvi_acc.py ├── scvi ├── __init__.py ├── benchmark.py ├── dataset │ ├── .DS_Store │ ├── BICCN.py │ ├── MouseBrain.py │ ├── __init__.py │ ├── anndata.py │ ├── brain_large.py │ ├── cite_seq.py │ ├── cortex.py │ ├── csv.py │ ├── dataset.py │ ├── dataset10X.py │ ├── hemato.py │ ├── loom.py │ ├── muris_tabula.py │ ├── paul_tusi.py │ ├── pbmc.py │ ├── scanorama.py │ ├── seqfish.py │ ├── smfish.py │ └── synthetic.py ├── harmonization │ ├── .DS_Store │ ├── DEfunctions.py │ ├── IDR.py │ ├── __init__.py │ ├── classification │ │ ├── CORAL.py │ │ ├── JDA.py │ │ ├── __init__.py │ │ ├── rf.py │ │ ├── scmap.py │ │ └── svc.py │ ├── clustering │ │ ├── MNN.py │ │ ├── Magan.py │ │ ├── R │ │ │ └── Seurat.functions.R │ │ ├── __init__.py │ │ ├── combat.py │ │ ├── seurat.py │ │ └── simlr.py │ └── utils_chenling.py ├── inference │ ├── __init__.py │ ├── annotation.py │ ├── fish.py │ ├── inference.py │ ├── posterior.py │ └── trainer.py ├── metrics │ ├── IDR.py │ ├── __init__.py │ ├── adapt_encoder.py │ ├── classification.py │ ├── clustering.py │ ├── differential_expression.py │ ├── early_stopping.py │ ├── imputation.py │ ├── log_likelihood.py │ └── visualization.py └── models │ ├── __init__.py │ ├── classifier.py │ ├── log_likelihood.py │ ├── modules.py │ ├── scanvi.py │ ├── utils.py │ ├── vae.py │ ├── vae_fish.py │ └── vaec.py ├── setup.cfg ├── setup.py ├── simulation_benchmark.py ├── test.py ├── tests ├── .DS_Store ├── notebooks │ ├── annotation.config.json │ ├── basic_tutorial.config.json │ ├── data_loading.config.json │ ├── scRNA_and_smFISH.config.json │ └── scVI-reproducibility.config.json ├── test_notebook.py └── test_scvi.py └── tox.ini /.DS_Store: -------------------------------------------------------------------------------- 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