├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ ├── feature_request.md │ └── new_task.yml ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── integration-test.yml │ ├── main-build.yml │ ├── release-build.yml │ └── viash-test.yml ├── .gitignore ├── .vscode └── settings.json ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── CONTRIBUTING.qmd ├── LICENSE ├── README.md ├── _viash.yaml ├── main.nf ├── nextflow.config └── src ├── common ├── check_dataset_schema │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── check_yaml_schema │ ├── config.vsh.yaml │ └── script.py ├── comp_tests │ ├── check_get_info.py │ ├── check_method_config.py │ ├── check_metric_config.py │ └── run_and_check_adata.py ├── create_component │ ├── config.vsh.yaml │ ├── script.py │ ├── script.sh │ └── test.py ├── create_task_readme │ ├── config.vsh.yaml │ ├── render_all.sh │ ├── script.R │ └── test.R ├── decompress_gzip │ ├── config.vsh.yaml │ ├── script.sh │ └── test.sh ├── extract_metadata │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── extract_scores │ ├── config.vsh.yaml │ └── script.R ├── helper_functions │ ├── read_and_merge_yaml.R │ ├── read_and_merge_yaml.py │ ├── read_anndata_partial.py │ ├── read_api_files.R │ ├── setup_logger.py │ ├── strip_margin.R │ ├── strip_margin.py │ └── subset_anndata.py ├── library.bib ├── ontology │ └── check_obsolete_terms │ │ ├── config.vsh.yaml │ │ ├── script.R │ │ └── test.R ├── process_dataset_metadata │ └── run │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run.sh ├── process_task_results │ ├── api │ │ └── get_info.yaml │ ├── generate_qc │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── get_api_info │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── get_dataset_info │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── get_method_info │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── get_metric_info │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── get_results │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── get_task_info │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── run │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ ├── run_nf_tower_test.sh │ │ └── run_test.sh │ └── yaml_to_json │ │ ├── config.vsh.yaml │ │ └── script.py ├── resources_test_scripts │ ├── aws_sync.sh │ └── task_metadata.sh ├── schemas │ ├── api_component.yaml │ ├── api_file.yaml │ ├── defs_common.yaml │ ├── defs_viash.yaml │ ├── task_control_method.yaml │ ├── task_info.yaml │ ├── task_method.yaml │ └── task_metric.yaml └── sync_test_resources │ ├── config.vsh.yaml │ ├── run_test.sh │ └── script.sh ├── datasets ├── README.md ├── README.qmd ├── api │ ├── README.md │ ├── README.qmd │ ├── comp_dataset_loader.yaml │ ├── comp_normalization.yaml │ ├── comp_processor_hvg.yaml │ ├── comp_processor_knn.yaml │ ├── comp_processor_pca.yaml │ ├── comp_processor_subset.yaml │ ├── comp_processor_svd.yaml │ ├── file_common_dataset.yaml │ ├── file_hvg.yaml │ ├── file_knn.yaml │ ├── file_multimodal_dataset.yaml │ ├── file_normalized.yaml │ ├── file_pca.yaml │ ├── file_raw.yaml │ └── file_svd.yaml ├── loaders │ ├── cellxgene_census │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── cellxgene_census_from_source_h5ad │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── openproblems_neurips2021_bmmc │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── openproblems_neurips2022_pbmc │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── openproblems_v1 │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── openproblems_v1_multimodal │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── tenx_visium │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ ├── zenodo_spatial │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py │ └── zenodo_spatial_slidetags │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test.py ├── normalization │ ├── atac_tfidf │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── l1_sqrt │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── log_cp │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── log_scran_pooling │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── prot_clr │ │ ├── config.vsh.yaml │ │ └── script.py │ └── sqrt_cp │ │ ├── config.vsh.yaml │ │ └── script.py ├── processors │ ├── hvg │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── knn │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── pca │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── subsample │ │ ├── config.vsh.yaml │ │ ├── script.py │ │ └── test_script.py │ └── svd │ │ ├── config.vsh.yaml │ │ └── script.py ├── resource_scripts │ ├── cellxgene_census.sh │ ├── dataset_info.sh │ ├── openproblems_neurips2021_multimodal.sh │ ├── openproblems_neurips2021_multimodal_test.sh │ ├── openproblems_neurips2022_pbmc.sh │ ├── openproblems_v1.sh │ ├── openproblems_v1_multimodal.sh │ ├── openproblems_v1_multimodal_test.sh │ ├── openproblems_v1_test.sh │ ├── tenx_visium.sh │ ├── zenodo_spatial.sh.sh │ └── zenodo_spatial_slidetags.sh ├── resource_test_scripts │ ├── cxg_mouse_pancreas_atlas.sh │ ├── mouse_brain_coronal_section1.sh │ ├── neurips2021_bmmc.sh │ ├── neurips2022_pbmc.sh │ ├── pancreas.sh │ ├── scicar_cell_lines.sh │ └── slideseq_test.sh └── workflows │ ├── extract_dataset_info │ ├── config.vsh.yaml │ ├── main.nf │ └── run_test.sh │ ├── extract_dataset_meta │ ├── config.vsh.yaml │ ├── main.nf │ └── run_test.sh │ ├── process_cellxgene_census │ ├── config.vsh.yaml │ └── main.nf │ ├── process_openproblems_neurips2021_bmmc │ ├── config.vsh.yaml │ └── main.nf │ ├── process_openproblems_neurips2022_pbmc │ ├── config.vsh.yaml │ └── main.nf │ ├── process_openproblems_v1 │ ├── config.vsh.yaml │ └── main.nf │ ├── process_openproblems_v1_multimodal │ ├── config.vsh.yaml │ └── main.nf │ ├── process_tenx_visium │ ├── config.vsh.yaml │ └── main.nf │ ├── process_zenodo_spatial │ ├── config.vsh.yaml │ └── main.nf │ └── process_zenodo_spatial_slidetags │ ├── config.vsh.yaml │ └── main.nf ├── migration ├── check_migration.sh ├── check_migration_status │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── list_git_shas │ ├── config.vsh.yaml │ ├── script.py │ └── test.py └── update_bibtex │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── tasks ├── batch_integration │ ├── README.md │ ├── api │ │ ├── comp_control_method_embedding.yaml │ │ ├── comp_control_method_feature.yaml │ │ ├── comp_control_method_graph.yaml │ │ ├── comp_method_embedding.yaml │ │ ├── comp_method_feature.yaml │ │ ├── comp_method_graph.yaml │ │ ├── comp_metric_embedding.yaml │ │ ├── comp_metric_feature.yaml │ │ ├── comp_metric_graph.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── comp_transformer_embedding_to_graph.yaml │ │ ├── comp_transformer_feature_to_embedding.yaml │ │ ├── file_common_dataset.yaml │ │ ├── file_dataset.yaml │ │ ├── file_integrated_embedding.yaml │ │ ├── file_integrated_feature.yaml │ │ ├── file_integrated_graph.yaml │ │ ├── file_score.yaml │ │ ├── file_solution.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── no_integration │ │ │ ├── batch_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── global_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── global_feature │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ └── global_graph │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ ├── perfect_integration │ │ │ ├── celltype_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ └── celltype_jitter_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ ├── random_integration │ │ │ ├── batch_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── batch_feature │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── batch_graph │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── celltype_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── celltype_feature │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── celltype_graph │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── global_embed │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ ├── global_feature │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ │ └── global_graph │ │ │ │ ├── config.vsh.yaml │ │ │ │ └── script.py │ │ └── utils.py │ ├── methods │ │ ├── bbknn │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── combat │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── fastmnn_embedding │ │ │ └── config.vsh.yaml │ │ ├── fastmnn_feature │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── liger │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── mnn_correct │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── mnnpy │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── pyliger │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── scalex_embed │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── scalex_feature │ │ │ └── config.vsh.yaml │ │ ├── scanorama_embed │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── scanorama_feature │ │ │ └── config.vsh.yaml │ │ ├── scanvi │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── scvi │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ ├── asw_batch │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── asw_label │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── cell_cycle_conservation │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── clustering_overlap │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── graph_connectivity │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── hvg_overlap │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── isolated_label_asw │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── isolated_label_f1 │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── kbet │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── lisi │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── pcr │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ ├── run_benchmark.sh │ │ └── run_benchmark_test.sh │ ├── resources_test_scripts │ │ └── process.sh │ ├── transformers │ │ ├── embed_to_graph │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── feature_to_embed │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_nextflow.sh │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── denoising │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset.yaml │ │ ├── file_denoised.yaml │ │ ├── file_score.yaml │ │ ├── file_test.yaml │ │ ├── file_train.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── no_denoising │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── perfect_denoising │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── methods │ │ ├── alra │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── dca │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── knn_smoothing │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── magic │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── saver │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ ├── metrics │ │ ├── mse │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── poisson │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ ├── helper.py │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ ├── run_benchmark.sh │ │ └── run_benchmark_test.sh │ ├── resources_test_scripts │ │ └── pancreas.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── dimensionality_reduction │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset.yaml │ │ ├── file_dataset.yaml │ │ ├── file_embedding.yaml │ │ ├── file_score.yaml │ │ ├── file_solution.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── random_features │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── spectral_features │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── true_features │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── methods │ │ ├── densmap │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── diffusion_map │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── ivis │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── lmds │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── neuralee │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── pca │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── phate │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── pymde │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── simlr │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── tsne │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── umap │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ ├── clustering_performance │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── coranking │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── density_preservation │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── distance_correlation │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── trustworthiness │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ ├── run_benchmark.sh │ │ └── run_benchmark_test.sh │ ├── resources_test_scripts │ │ └── pancreas.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── label_projection │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset.yaml │ │ ├── file_prediction.yaml │ │ ├── file_score.yaml │ │ ├── file_solution.yaml │ │ ├── file_test.yaml │ │ ├── file_train.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── majority_vote │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── random_labels │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── true_labels │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── methods │ │ ├── knn │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── logistic_regression │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── mlp │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── naive_bayes │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── scanvi │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── scanvi_scarches │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── seurat_transferdata │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ └── xgboost │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ ├── accuracy │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── f1 │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ ├── run_benchmark.sh │ │ └── run_benchmark_test.sh │ ├── resources_test_scripts │ │ └── pancreas.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ └── main.nf │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── match_modalities │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset_mod1.yaml │ │ ├── file_common_dataset_mod2.yaml │ │ ├── file_dataset_mod1.yaml │ │ ├── file_dataset_mod2.yaml │ │ ├── file_integrated_mod1.yaml │ │ ├── file_integrated_mod2.yaml │ │ ├── file_score.yaml │ │ ├── file_solution_mod1.yaml │ │ ├── file_solution_mod2.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── random_features │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── true_features │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── methods │ │ ├── fastmnn │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── harmonic_alignment │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── procrustes │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── scot │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ ├── knn_auc │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── mse │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ └── run_benchmark.sh │ ├── resources_test_scripts │ │ └── scicar_cell_lines.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ └── main.nf │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── predict_modality │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_method_predict.yaml │ │ ├── comp_method_train.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset_mod1.yaml │ │ ├── file_common_dataset_mod2.yaml │ │ ├── file_prediction.yaml │ │ ├── file_pretrained_model.yaml │ │ ├── file_score.yaml │ │ ├── file_test_mod1.yaml │ │ ├── file_test_mod2.yaml │ │ ├── file_train_mod1.yaml │ │ ├── file_train_mod2.yaml │ │ ├── task_info.yaml │ │ └── thumbnail.svg │ ├── control_methods │ │ ├── meanpergene │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── random_predict │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── solution │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ └── zeros │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── methods │ │ ├── guanlab_dengkw_pm │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── knnr_py │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── knnr_r │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── lm │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── lmds_irlba_rf │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── newwave_knnr │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── novel │ │ │ ├── helper_functions.py │ │ │ ├── predict │ │ │ │ ├── config.vsh.yaml │ │ │ │ ├── run_test.sh │ │ │ │ └── script.py │ │ │ ├── run │ │ │ │ ├── config.vsh.yaml │ │ │ │ ├── main.nf │ │ │ │ └── run_test.sh │ │ │ └── train │ │ │ │ ├── config.vsh.yaml │ │ │ │ ├── run_test.sh │ │ │ │ └── script.py │ │ ├── random_forest │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ └── simple_mlp │ │ │ ├── predict │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ │ ├── resources │ │ │ ├── models.py │ │ │ ├── utils.py │ │ │ └── yaml │ │ │ │ ├── mlp_ADT2GEX.yaml │ │ │ │ ├── mlp_ATAC2GEX.yaml │ │ │ │ └── mlp_GEX2ADT.yaml │ │ │ ├── run │ │ │ ├── config.vsh.yaml │ │ │ ├── main.nf │ │ │ └── run_test.sh │ │ │ ├── test.sh │ │ │ └── train │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ ├── correlation │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ └── mse │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ └── run_benchmark.sh │ ├── resources_test_scripts │ │ └── neurips2021_bmmc.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh ├── spatial_decomposition │ ├── README.md │ ├── api │ │ ├── comp_control_method.yaml │ │ ├── comp_method.yaml │ │ ├── comp_metric.yaml │ │ ├── comp_process_dataset.yaml │ │ ├── file_common_dataset.yaml │ │ ├── file_output.yaml │ │ ├── file_score.yaml │ │ ├── file_single_cell.yaml │ │ ├── file_solution.yaml │ │ ├── file_spatial_masked.yaml │ │ └── task_info.yaml │ ├── control_methods │ │ ├── random_proportions │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── true_proportions │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── dataset_simulator │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── methods │ │ ├── cell2location │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── destvi │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── nmfreg │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── nnls │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── rctd │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── seurat │ │ │ ├── config.vsh.yaml │ │ │ └── script.R │ │ ├── stereoscope │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ ├── tangram │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ │ └── vanillanmf │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── metrics │ │ └── r2 │ │ │ ├── config.vsh.yaml │ │ │ └── script.py │ ├── process_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ │ ├── process_datasets.sh │ │ └── run_benchmark.sh │ ├── resources_test_scripts │ │ ├── cxg_mouse_pancreas_atlas.sh │ │ └── pancreas.sh │ └── workflows │ │ ├── process_datasets │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh │ │ └── run_benchmark │ │ ├── config.vsh.yaml │ │ ├── main.nf │ │ └── run_test.sh └── spatially_variable_genes │ ├── README.md │ ├── api │ ├── comp_control_method.yaml │ ├── comp_method.yaml │ ├── comp_metric.yaml │ ├── comp_process_dataset.yaml │ ├── file_common_dataset.yaml │ ├── file_dataset.yaml │ ├── file_output.yaml │ ├── file_score.yaml │ ├── file_simulated_dataset.yaml │ ├── file_solution.yaml │ └── task_info.yaml │ ├── control_methods │ ├── random_ranking │ │ ├── config.vsh.yaml │ │ └── script.py │ └── true_ranking │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── methods │ ├── boostgp │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── gpcounts │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── moran_i │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── nnsvg │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── scgco │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── sepal │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── somde │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── spagcn │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── spagft │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── spanve │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── spark │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── spark_x │ │ ├── config.vsh.yaml │ │ └── script.R │ ├── spatialde │ │ ├── config.vsh.yaml │ │ └── script.py │ └── spatialde2 │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── metrics │ └── correlation │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── process_dataset │ ├── select_reference │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── simulate_svg │ │ ├── config.vsh.yaml │ │ └── script.R │ └── split_dataset │ │ ├── config.vsh.yaml │ │ └── script.py │ ├── resources_scripts │ ├── process_datasets.sh │ └── run_benchmark.sh │ ├── resources_test_scripts │ └── mouse_brain_coronal_section1.sh │ └── workflows │ ├── process_datasets │ ├── config.vsh.yaml │ ├── main.nf │ └── run_test.sh │ └── run_benchmark │ ├── config.vsh.yaml │ ├── main.nf │ └── run_test.sh └── wf_utils ├── ProfilesHelper.config ├── helper.nf ├── labels.config ├── labels_ci.config └── 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