.gitignore
README.md
UTSW_License.txt
setup.py
Experiments/AML/paths_config.py
Experiments/AML/preprocessing/AML_data_reader.ipynb
Experiments/AML/preprocessing/preprocess_AML.py
Experiments/AML/preprocessing/sbatch_preprocess_AML.sh
Experiments/AML/preprocessing/supplemental_AML.ipynb
Experiments/AML/preprocessing/5fold_cross_val/check_splits.ipynb
Experiments/AML/preprocessing/5fold_cross_val/config_split_paths.py
Experiments/AML/preprocessing/5fold_cross_val/create_splits.ipynb
Experiments/AML/run_models/AE/model_config.py
Experiments/AML/run_models/AE/run_AE_allfolds.py
Experiments/AML/run_models/AE/sbatch_run_AE.sh
Experiments/AML/run_models/AEC/model_config.py
Experiments/AML/run_models/AEC/run_AEC_allfolds.py
Experiments/AML/run_models/AEC/sbatch_run_AEC.sh
Experiments/AML/run_models/MEC/celltype_target/PCA_latent/mec_allfolds.py
Experiments/AML/run_models/MEC/celltype_target/PCA_latent/model_config.py
Experiments/AML/run_models/MEC/celltype_target/scMEDAL-FE_latent/mec_allfolds.py
Experiments/AML/run_models/MEC/celltype_target/scMEDAL-FE_latent/model_config.py
Experiments/AML/run_models/MEC/celltype_target/scMEDAL-FE_latent/sbatch_run_MEC.sh
Experiments/AML/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/mec_allfolds.py
Experiments/AML/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/model_config.py
Experiments/AML/run_models/compare_results/clustering_scores/compare_clustering_scores.py
Experiments/AML/run_models/compare_results/genomaps/pipeline_CMmultibatch_genomap_and_plot_multicell.py
Experiments/AML/run_models/compare_results/genomaps/sbatch_get_genomaps.sh
Experiments/AML/run_models/compare_results/umap_plots/sbatch_compare_results_umap.sh
Experiments/AML/run_models/scMEDAL-FE/model_config.py
Experiments/AML/run_models/scMEDAL-FE/run_scMEDAL-FE_allfolds.py
Experiments/AML/run_models/scMEDAL-FE/sbatch_run_scMEDAL-FE_allfolds.sh
Experiments/AML/run_models/scMEDAL-FEC/model_config.py
Experiments/AML/run_models/scMEDAL-FEC/run_scMEDAL-FEC_allfolds.py
Experiments/AML/run_models/scMEDAL-FEC/sbatch_run_scMEDAL-FEC_allfolds.sh
Experiments/AML/run_models/scMEDAL-RE/model_config.py
Experiments/ASD/paths_config.py
Experiments/ASD/preprocessing/preprocess_ASD.py
Experiments/ASD/preprocessing/sbatch_preprocess_ASD.sh
Experiments/ASD/preprocessing/5fold_cross_val/check_splits.ipynb
Experiments/ASD/preprocessing/5fold_cross_val/config_split_paths.py
Experiments/ASD/preprocessing/5fold_cross_val/create_splits.ipynb
Experiments/ASD/run_models/AE/model_config.py
Experiments/ASD/run_models/AE/run_AE_allfolds.py
Experiments/ASD/run_models/AE/sbatch_run_AE.sh
Experiments/ASD/run_models/AEC/model_config.py
Experiments/ASD/run_models/AEC/run_AEC_allfolds.py
Experiments/ASD/run_models/AEC/sbatch_run_AEC.sh
Experiments/ASD/run_models/MEC/celltype_target/PCA_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/celltype_target/PCA_latent/model_config.py
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FE_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FE_latent/model_config.py
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FE_latent/sbatch_run_MEC.sh
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/model_config.py
Experiments/ASD/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/sbatch_run_MEC.sh
Experiments/ASD/run_models/MEC/dx_target/PCA_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/dx_target/PCA_latent/model_config.py
Experiments/ASD/run_models/MEC/dx_target/PCA_latent/sbatch_run_MEC.sh
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FE_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FE_latent/model_config.py
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FE_latent/sbatch_run_MEC.sh
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FEandscMEDAL-RE_latent/mec_allfolds.py
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FEandscMEDAL-RE_latent/model_config.py
Experiments/ASD/run_models/MEC/dx_target/scMEDAL-FEandscMEDAL-RE_latent/sbatch_run_MEC.sh
Experiments/ASD/run_models/compare_results/clustering_scores/compare_clustering_scores.py
Experiments/ASD/run_models/compare_results/genomaps/pipeline_CMmultibatch_genomap_and_plot.py
Experiments/ASD/run_models/compare_results/genomaps/sbatch_get_genomaps.sh
Experiments/ASD/run_models/compare_results/umap_plots/sbatch_compare_results_umap.sh
Experiments/ASD/run_models/scMEDAL-FE/model_config.py
Experiments/ASD/run_models/scMEDAL-FE/run_scMEDAL-FE_allfolds.py
Experiments/ASD/run_models/scMEDAL-FE/sbatch_run_scMEDAL-FE_allfolds.sh
Experiments/ASD/run_models/scMEDAL-FEC/model_config.py
Experiments/ASD/run_models/scMEDAL-FEC/run_scMEDAL-FEC_allfolds.py
Experiments/ASD/run_models/scMEDAL-FEC/sbatch_run_scMEDAL-FEC_allfolds.sh
Experiments/ASD/run_models/scMEDAL-RE/model_config.py
Experiments/ASD/run_models/scMEDAL-RE/run_scMEDAL-RE_allfolds.py
Experiments/ASD/run_models/scMEDAL-RE/sbatch_run_scMEDAL-RE_allfolds.sh
Experiments/HealthyHeart/paths_config.py
Experiments/HealthyHeart/preprocessing/preprocessing_HealthyHeart.ipynb
Experiments/HealthyHeart/preprocessing/visualizing_HealthyHeart.ipynb
Experiments/HealthyHeart/preprocessing/5fold_cross_val/check_splits.ipynb
Experiments/HealthyHeart/preprocessing/5fold_cross_val/config_split_paths.py
Experiments/HealthyHeart/preprocessing/5fold_cross_val/create_splits.ipynb
Experiments/HealthyHeart/run_models/AE/model_config.py
Experiments/HealthyHeart/run_models/AE/run_AE_allfolds.py
Experiments/HealthyHeart/run_models/AE/sbatch_run_AE.sh
Experiments/HealthyHeart/run_models/AEC/model_config.py
Experiments/HealthyHeart/run_models/AEC/run_AEC_allfolds.py
Experiments/HealthyHeart/run_models/AEC/sbatch_run_AEC.sh
Experiments/HealthyHeart/run_models/MEC/celltype_target/PCA_latent/mec_allfolds.py
Experiments/HealthyHeart/run_models/MEC/celltype_target/PCA_latent/model_config.py
Experiments/HealthyHeart/run_models/MEC/celltype_target/scMEDAL-FE_latent/mec_allfolds.py
Experiments/HealthyHeart/run_models/MEC/celltype_target/scMEDAL-FE_latent/model_config.py
Experiments/HealthyHeart/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/mec_allfolds.py
Experiments/HealthyHeart/run_models/MEC/celltype_target/scMEDAL-FEandscMEDAL-RE_latent/model_config.py
Experiments/HealthyHeart/run_models/compare_results/clustering_scores/compare_clustering_scores.py
Experiments/HealthyHeart/run_models/compare_results/genomaps/pipeline_CMmultibatch_genomap_and_plot_multicell.py
Experiments/HealthyHeart/run_models/compare_results/genomaps/sbatch_get_genomaps.sh
Experiments/HealthyHeart/run_models/compare_results/umap_plots/compare_results_umap.py
Experiments/HealthyHeart/run_models/compare_results/umap_plots/sbatch_compare_results_umap.sh
Experiments/HealthyHeart/run_models/scMEDAL-FE/model_config.py
Experiments/HealthyHeart/run_models/scMEDAL-FE/run_scMEDAL-FE_allfolds.py
Experiments/HealthyHeart/run_models/scMEDAL-FE/sbatch_run_scMEDAL-FE_allfolds.sh
Experiments/HealthyHeart/run_models/scMEDAL-FEC/model_config.py
Experiments/HealthyHeart/run_models/scMEDAL-FEC/run_scMEDAL-FEC_allfolds.py
Experiments/HealthyHeart/run_models/scMEDAL-FEC/sbatch_run_scMEDAL-FEC_allfolds.sh
Experiments/HealthyHeart/run_models/scMEDAL-RE/model_config.py
Experiments/HealthyHeart/run_models/scMEDAL-RE/run_scMEDAL-RE_allfolds.py
Experiments/HealthyHeart/run_models/scMEDAL-RE/sbatch_run_scMEDAL-RE_allfolds.sh
docs/ExperimentOutputs.md
docs/ExperimentsReproducibility.md
docs/How2AnalyzeYourModelOutputs.md
docs/How2RunYourExpt.md
docs/How2SetupYourExpt.md
docs/images/.gitkeep
docs/images/scMEDAL.png
scMEDAL/__init__.py
scMEDAL.egg-info/PKG-INFO
scMEDAL.egg-info/SOURCES.txt
scMEDAL.egg-info/dependency_links.txt
scMEDAL.egg-info/top_level.txt
scMEDAL/models/__init__.py
scMEDAL/models/random_effects.py
scMEDAL/models/scMEDAL.py
scMEDAL/scMEDAL.egg-info/PKG-INFO
scMEDAL/scMEDAL.egg-info/SOURCES.txt
scMEDAL/scMEDAL.egg-info/dependency_links.txt
scMEDAL/scMEDAL.egg-info/top_level.txt
scMEDAL/utils/__init__.py
scMEDAL/utils/callbacks.py
scMEDAL/utils/compare_results_utils.py
scMEDAL/utils/genomaps_utils.py
scMEDAL/utils/model_train_utils.py
scMEDAL/utils/preprocessing_utils.py
scMEDAL/utils/splitter.py
scMEDAL/utils/utils.py
scMEDAL/utils/utils_load_model.py
scMEDAL_env/genomaps_env.yaml
scMEDAL_env/preprocess_and_plot_umaps_env.yaml
scMEDAL_env/run_models_env.yaml