├── .github ├── dependabot.yml └── workflows │ ├── release.yml │ ├── test.yml │ └── test_examples.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .yamllint.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── dance ├── __init__.py ├── atlas │ ├── data_dropbox_upload.py │ └── sc_similarity │ │ └── anndata_similarity.py ├── config.py ├── data │ ├── __init__.py │ └── base.py ├── datasets │ ├── __init__.py │ ├── base.py │ ├── multimodality.py │ ├── singlemodality.py │ └── spatial.py ├── exceptions.py ├── metadata │ ├── clustering.csv │ ├── imputation.csv │ ├── imputation.py │ └── scdeepsort.csv ├── models │ ├── __init__.py │ └── nn │ │ ├── __init__.py │ │ ├── gnn.py │ │ └── mlp.py ├── modules │ ├── __init__.py │ ├── base.py │ ├── multi_modality │ │ ├── __init__.py │ │ ├── joint_embedding │ │ │ ├── __init__.py │ │ │ ├── dcca.py │ │ │ ├── jae.py │ │ │ ├── scmogcn.py │ │ │ ├── scmogcnv2.py │ │ │ └── scmvae.py │ │ ├── match_modality │ │ │ ├── __init__.py │ │ │ ├── cmae.py │ │ │ ├── scmm.py │ │ │ └── scmogcn.py │ │ └── predict_modality │ │ │ ├── __init__.py │ │ │ ├── babel.py │ │ │ ├── cmae.py │ │ │ ├── scmm.py │ │ │ └── scmogcn.py │ ├── single_modality │ │ ├── __init__.py │ │ ├── cell_type_annotation │ │ │ ├── __init__.py │ │ │ ├── actinn.py │ │ │ ├── celltypist.py │ │ │ ├── scdeepsort.py │ │ │ ├── scheteronet.py │ │ │ ├── singlecellnet.py │ │ │ └── svm.py │ │ ├── clustering │ │ │ ├── __init__.py │ │ │ ├── graphsc.py │ │ │ ├── scdcc.py │ │ │ ├── scdeepcluster.py │ │ │ ├── scdsc.py │ │ │ └── sctag.py │ │ └── imputation │ │ │ ├── __init__.py │ │ │ ├── deepimpute.py │ │ │ ├── graphsci.py │ │ │ ├── magic.py │ │ │ └── scgnn2.py │ └── spatial │ │ ├── __init__.py │ │ ├── cell_type_deconvo │ │ ├── __init__.py │ │ ├── card.py │ │ ├── dstg.py │ │ ├── spatialdecon.py │ │ ├── spotlight.py │ │ └── stdgcn.py │ │ └── spatial_domain │ │ ├── EfNST.py │ │ ├── __init__.py │ │ ├── louvain.py │ │ ├── spagcn.py │ │ ├── stagate.py │ │ └── stlearn.py ├── pipeline.py ├── plotting │ └── __init__.py ├── registry.py ├── settings.py ├── transforms │ ├── __init__.py │ ├── base.py │ ├── cell_feature.py │ ├── filter.py │ ├── gene_holdout.py │ ├── graph │ │ ├── __init__.py │ │ ├── cell_feature_graph.py │ │ ├── dstg_graph.py │ │ ├── feature_feature_graph.py │ │ ├── heteronet_graph.py │ │ ├── neighbor_graph.py │ │ ├── resept_graph.py │ │ ├── scmogcn_graph.py │ │ └── spatial_graph.py │ ├── graph_construct.py │ ├── interface.py │ ├── mask.py │ ├── misc.py │ ├── normalize.py │ ├── preprocess.py │ ├── pseudobulk.py │ ├── sc3_feature.py │ ├── scn_feature.py │ ├── spatial_feature.py │ └── stats.py ├── typing.py └── utils │ ├── __init__.py │ ├── download.py │ ├── io.py │ ├── loss.py │ ├── matrix.py │ ├── metrics.py │ ├── preprocess.py │ ├── regular.py │ ├── status.py │ └── wrappers.py ├── docker ├── Dockerfile └── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── DANCE 2.0 │ ├── Preprocessing Steps and Available Function Candidates.rst │ ├── Search Space of Preprocessing Function Parameters.rst │ ├── experiments │ │ ├── celltype_annotation │ │ │ ├── actinn.rst │ │ │ ├── celltypist.rst │ │ │ ├── index.rst │ │ │ ├── scdeepsort.rst │ │ │ ├── scheteronet.rst │ │ │ ├── singlecellnet.rst │ │ │ └── svm.rst │ │ ├── celltype_deconvolution │ │ │ ├── card.rst │ │ │ ├── dstg.rst │ │ │ ├── index.rst │ │ │ ├── spatialdecon.rst │ │ │ ├── spotlight.rst │ │ │ └── stdgcn.rst │ │ ├── cluster │ │ │ ├── graphsc_config.rst │ │ │ ├── index.rst │ │ │ ├── scdcc_config.rst │ │ │ ├── scdeepcluster_config.rst │ │ │ ├── scdsc_config.rst │ │ │ └── sctag_config.rst │ │ ├── imputation │ │ │ ├── deepimpute.rst │ │ │ ├── graphsci.rst │ │ │ ├── index.rst │ │ │ └── scgnn2.rst │ │ ├── index.rst │ │ ├── joint_embedding │ │ │ ├── dcca.rst │ │ │ ├── index.rst │ │ │ ├── jae.rst │ │ │ ├── scmogcn.rst │ │ │ └── scmvae.rst │ │ └── spatial_domain │ │ │ ├── EfNST.rst │ │ │ ├── index.rst │ │ │ ├── louvain.rst │ │ │ ├── spagcn.rst │ │ │ ├── stagate.rst │ │ │ └── stlearn.rst │ ├── index.rst │ └── tutorials │ │ └── tutorial.ipynb │ ├── api │ ├── atlas.rst │ ├── data.rst │ ├── datasets.rst │ ├── search.rst │ ├── transforms.graph.rst │ └── transforms.rst │ ├── conf.py │ ├── index.rst │ └── modules │ ├── multi_modality.rst │ ├── single_modality.rst │ └── spatial.rst ├── examples ├── atlas │ ├── Cell Type Annotation Atlas_origin.xlsx │ ├── __init__.py │ ├── config │ │ ├── atlas_template_yamls │ │ │ ├── cta_actinn │ │ │ │ └── pipeline_params_tuning_config.yaml │ │ │ ├── cta_celltypist │ │ │ │ └── pipeline_params_tuning_config.yaml │ │ │ ├── cta_scdeepsort │ │ │ │ └── pipeline_params_tuning_config.yaml │ │ │ └── cta_singlecellnet │ │ │ │ └── pipeline_params_tuning_config.yaml │ │ ├── commands.yaml │ │ └── readme.md │ ├── demos │ │ ├── __init__.py │ │ └── main.py │ ├── get_result_web.py │ ├── results.xlsx │ ├── sc_similarity_examples │ │ ├── __init__.py │ │ ├── cache │ │ │ └── sweep_cache.json │ │ ├── configs │ │ │ └── exclude_dataset.json │ │ ├── data │ │ │ └── Cell Type Annotation Atlas.xlsx │ │ ├── data_processing │ │ │ ├── __init__.py │ │ │ └── merge_result_metadata.py │ │ ├── readme.md │ │ ├── run_similarity_optimization.sh │ │ ├── similarity │ │ │ ├── analyze_atlas_accuracy.py │ │ │ ├── example_usage_anndata.py │ │ │ ├── optimize_similarity_weights.py │ │ │ └── process_tissue_similarity_matrices.py │ │ └── visualization │ │ │ ├── __init__.py │ │ │ ├── vis_sim_v2_data.py │ │ │ ├── vis_sim_v2_vis.py │ │ │ ├── visualize_atlas_performance.py │ │ │ ├── visualize_atlas_performance_v2.py │ │ │ └── visualize_sim.py │ ├── setup_run.py │ ├── sweep_results │ │ ├── Blood_ans.csv │ │ ├── Brain_ans.csv │ │ ├── Heart_ans.csv │ │ ├── Intestine_ans.csv │ │ ├── Kidney_ans.csv │ │ ├── Lung_ans.csv │ │ └── Pancreas_ans.csv │ ├── temp.sh │ └── upload_data.py ├── dataset_server.json ├── heart_ans.csv ├── multi_modality │ ├── joint_embedding │ │ ├── dcca.py │ │ ├── jae.py │ │ ├── scmogcn.py │ │ ├── scmogcnv2.py │ │ └── scmvae.py │ ├── match_modality │ │ ├── cmae.py │ │ ├── scmm.py │ │ └── scmogcn.py │ └── predict_modality │ │ ├── babel.py │ │ ├── cmae.py │ │ ├── scmm.py │ │ └── scmogcn.py ├── readme.md ├── result_analysis │ ├── get_important_pattern.py │ ├── get_important_pattern_sweep.py │ └── get_num.py ├── single_modality │ ├── cell_type_annotation │ │ ├── actinn.py │ │ ├── celltypist.py │ │ ├── scdeepsort.py │ │ ├── scheteronet.py │ │ ├── singlecellnet.py │ │ └── svm.py │ ├── clustering │ │ ├── graphsc.py │ │ ├── scdcc.py │ │ ├── scdeepcluster.py │ │ ├── scdsc.py │ │ └── sctag.py │ └── imputation │ │ ├── deepimpute.py │ │ ├── graphsci.py │ │ ├── magic.py │ │ └── scgnn2.py ├── spatial │ ├── cell_type_deconvo │ │ ├── card.py │ │ ├── dstg.py │ │ ├── spatialdecon.py │ │ ├── spotlight.py │ │ └── stdgcn.py │ └── spatial_domain │ │ ├── EfNST.py │ │ ├── louvain.py │ │ ├── spagcn.py │ │ ├── stagate.py │ │ └── stlearn.py └── tuning │ ├── README.md │ ├── cluster_graphsc │ ├── human_pbmc2_cell │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cluster_scdcc │ ├── human_pbmc2_cell │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cluster_scdeepcluster │ ├── human_pbmc2_cell │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cluster_scdsc │ ├── human_pbmc2_cell │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cluster_sctag │ ├── human_pbmc2_cell │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cta_actinn │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_acc.csv │ └── main.py │ ├── cta_celltypist │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cta_scdeepsort │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cta_scheteronet │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cta_singlecellnet │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── cta_svm │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ ├── pipeline_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ ├── main.py │ ├── params_run.sh │ ├── params_tuning_config.yaml │ ├── pipeline_params_tuning_config.yaml │ ├── pipeline_run.sh │ ├── pipeline_tuning_config.yaml │ └── run.sh │ ├── custom-methods │ ├── 328_138 │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ └── 1_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ └── 1_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ ├── main.py │ └── tutorial.ipynb │ ├── deconv_card │ ├── hcc_liver │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── deconv_dstg │ ├── hcc_liver │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── deconv_spatialdecon │ ├── hcc_liver │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── deconv_spotlight │ ├── hcc_liver │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── deconv_stdgcn │ ├── hcc_liver │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── domain_EfNST │ ├── main.py │ └── sub_mba │ │ ├── config_yamls │ │ └── params │ │ │ ├── 0_params_tuning_config.yaml │ │ │ ├── 1_params_tuning_config.yaml │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ ├── params │ │ ├── 0_best.csv │ │ ├── 1_best.csv │ │ └── 2_best.csv │ │ └── pipeline │ │ └── best_test_acc.csv │ ├── domain_louvain │ ├── main.py │ └── sub_mba │ │ ├── config_yamls │ │ └── params │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ ├── params │ │ ├── 0_best_test_acc.csv │ │ ├── 1_best_test_acc.csv │ │ └── 2_best_test_acc.csv │ │ └── pipeline │ │ └── best_test_acc.csv │ ├── domain_spagcn │ ├── main.py │ └── sub_mba │ │ ├── config_yamls │ │ └── params │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ ├── params │ │ ├── 0_best_test_acc.csv │ │ ├── 1_best_test_acc.csv │ │ └── 2_best_test_acc.csv │ │ └── pipeline │ │ └── best_test_acc.csv │ ├── domain_stagate │ ├── main.py │ └── sub_mba │ │ ├── config_yamls │ │ └── params │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ ├── params │ │ ├── 0_best_test_acc.csv │ │ ├── 1_best_test_acc.csv │ │ └── 2_best_test_acc.csv │ │ └── pipeline │ │ └── best_test_acc.csv │ ├── domain_stlearn │ ├── main.py │ └── sub_mba │ │ ├── config_yamls │ │ └── params │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ ├── params │ │ ├── 0_best_test_acc.csv │ │ ├── 1_best_test_acc.csv │ │ └── 2_best_test_acc.csv │ │ └── pipeline │ │ └── best_test_acc.csv │ ├── handle_error.py │ ├── handle_sweep.py │ ├── imputation_deepimpute │ ├── human_melanoma_data │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ ├── 2_params_tuning_config.yaml │ │ │ │ ├── 3_params_tuning_config.yaml │ │ │ │ └── 4_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 2_best.csv │ │ │ ├── 3_best.csv │ │ │ └── 4_best.csv │ │ │ └── pipeline │ │ │ └── best.csv │ └── main.py │ ├── imputation_graphsci │ ├── human_melanoma_data │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ ├── 2_params_tuning_config.yaml │ │ │ │ ├── 3_params_tuning_config.yaml │ │ │ │ └── 4_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ ├── 2_best.csv │ │ │ ├── 3_best.csv │ │ │ └── 4_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── imputation_magic │ └── main.py │ ├── imputation_scgnn2 │ ├── human_melanoma_data │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ ├── 2_params_tuning_config.yaml │ │ │ │ ├── 3_params_tuning_config.yaml │ │ │ │ └── 4_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ ├── 2_best.csv │ │ │ ├── 3_best.csv │ │ │ └── 4_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── joint_embedding_dcca │ ├── GSE140203_SKIN_atac2gex │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best_test_acc.csv │ │ │ ├── 1_best_test_acc.csv │ │ │ └── 2_best_test_acc.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── joint_embedding_jae │ ├── GSE140203_SKIN_atac2gex │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best_test_acc.csv │ │ │ ├── 1_best_test_acc.csv │ │ │ └── 2_best_test_acc.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── joint_embedding_scmogcn │ ├── GSE140203_SKIN_atac2gex │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_test_acc_params_tuning_config.yaml │ │ │ │ ├── 1_test_acc_params_tuning_config.yaml │ │ │ │ └── 2_test_acc_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best_test_acc.csv │ │ │ ├── 1_best_test_acc.csv │ │ │ └── 2_best_test_acc.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── joint_embedding_scmvae │ ├── GSE140203_SKIN_atac2gex │ │ ├── config_yamls │ │ │ └── params │ │ │ │ ├── 0_params_tuning_config.yaml │ │ │ │ ├── 1_params_tuning_config.yaml │ │ │ │ └── 2_params_tuning_config.yaml │ │ ├── pipeline_params_tuning_config.yaml │ │ └── results │ │ │ ├── params │ │ │ ├── 0_best.csv │ │ │ ├── 1_best.csv │ │ │ └── 2_best.csv │ │ │ └── pipeline │ │ │ └── best_test_acc.csv │ └── main.py │ ├── predict_modality_babel │ └── main.py │ └── step3_default_params.yaml ├── imgs ├── dance_logo.jpg └── framework.png ├── install.sh ├── notebooks └── dance_data_tutorial.ipynb ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── atlas │ └── test_anndata_similarity.py ├── conftest.py ├── data │ └── test_data.py ├── setup │ ├── README.md │ └── run.sb ├── test.ipynb ├── test_bench.py ├── 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