.gitignore
.readthedocs.yml
.travis.yml
README.rst
__init__.py
requirements.txt
setup.py
docs/Makefile
docs/about.rst
docs/conf.py
docs/index.rst
docs/installation.rst
docs/make.bat
docs/model_sharing.rst
docs/requirements.txt
docs/training_tips.rst
docs/_static/custom.css
docs/api/dataset.rst
docs/api/index.rst
docs/api/models.rst
docs/api/plotting.rst
docs/api/utils.rst
notebooks/MARS_API.ipynb
notebooks/Pancreas.ipynb
notebooks/.ipynb_checkpoints/Pancreas-checkpoint.ipynb
notebooks/.ipynb_checkpoints/scanvi_m_surgery-checkpoint.ipynb
notebooks/.ipynb_checkpoints/scvi_m_surgery-checkpoint.ipynb
scArchest.egg-info/PKG-INFO
scArchest.egg-info/SOURCES.txt
scArchest.egg-info/dependency_links.txt
scArchest.egg-info/not-zip-safe
scArchest.egg-info/requires.txt
scArchest.egg-info/top_level.txt
scarchest/__init__.py
scarchest/dataset/__init__.py
scarchest/dataset/mars/__init__.py
scarchest/dataset/mars/meta_anndata.py
scarchest/dataset/scvi/__init__.py
scarchest/dataset/scvi/annotation_data_loader.py
scarchest/dataset/scvi/scvi_data_loader.py
scarchest/dataset/scvi/total_data_loader.py
scarchest/dataset/trvae/__init__.py
scarchest/dataset/trvae/_utils.py
scarchest/dataset/trvae/anndata.py
scarchest/dataset/trvae/data_handling.py
scarchest/metrics/__init__.py
scarchest/metrics/metrics.py
scarchest/models/__init__.py
scarchest/models/mars/__init__.py
scarchest/models/mars/activations.py
scarchest/models/mars/losses.py
scarchest/models/mars/mars.py
scarchest/models/scvi/__init__.py
scarchest/models/scvi/classifier.py
scarchest/models/scvi/scanvi.py
scarchest/models/scvi/scvi.py
scarchest/models/scvi/totalvi.py
scarchest/models/scvi/_base/__init__.py
scarchest/models/trvae/__init__.py
scarchest/models/trvae/_utils.py
scarchest/models/trvae/activations.py
scarchest/models/trvae/losses.py
scarchest/models/trvae/modules.py
scarchest/models/trvae/trvae.py
scarchest/plotting/__init__.py
scarchest/plotting/_alluvial.py
scarchest/plotting/sankey.py
scarchest/plotting/scvi_eval.py
scarchest/surgery/__init__.py
scarchest/surgery/mars.py
scarchest/surgery/scvi.py
scarchest/surgery/trvae.py
scarchest/trainers/__init__.py
scarchest/trainers/mars/__init__.py
scarchest/trainers/mars/_utils.py
scarchest/trainers/mars/mars_meta_trainer.py
scarchest/trainers/mars/meta.py
scarchest/trainers/mars/unsupervised.py
scarchest/trainers/scvi/__init__.py
scarchest/trainers/scvi/annotation.py
scarchest/trainers/scvi/inference.py
scarchest/trainers/scvi/total_inference.py
scarchest/trainers/scvi/trainer.py
scarchest/trainers/trvae/__init__.py
scarchest/trainers/trvae/_utils.py
scarchest/trainers/trvae/trainer.py
scarchest/trainers/trvae/unsupervised.py
scarchest/utils/__init__.py
scarchest/utils/monitor.py
scarchest/utils/scvi/__init__.py
scarchest/utils/scvi/_constants.py
scarchest/utils/scvi/_settings.py
tests/__init__.py
tests/mars/__init__.py
tests/mars/mars.py
tests/scvi_tests/scanvi_surgery_notebook.py
tests/scvi_tests/scvi_surgery_notebook.py
tests/scvi_tests/totalvi_surgery_notebook.py
tests/scvi_tests/figure_2/only_query.py
tests/scvi_tests/figure_2/plotting.py
tests/scvi_tests/figure_2/predict.py
tests/scvi_tests/figure_2/surgery.py
tests/scvi_tests/sfaira_organ_testing/create_h5ad_file.py
tests/scvi_tests/sfaira_organ_testing/mouse_pancreas/only_query.py
tests/trvae_tests/batch_loading_test.py
tests/trvae_tests/trvae_test.py