.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/zenodo.rst
notebooks/scanvi_surgery_pipeline.ipynb
notebooks/scvi_surgery_pipeline.ipynb
notebooks/totalvi_surgery_pipeline.ipynb
notebooks/trVAE_zenodo_pipeline.ipynb
notebooks/trvae_surgery_pipeline.ipynb
scArches.egg-info/PKG-INFO
scArches.egg-info/SOURCES.txt
scArches.egg-info/dependency_links.txt
scArches.egg-info/not-zip-safe
scArches.egg-info/requires.txt
scArches.egg-info/top_level.txt
scarches/__init__.py
scarches/dataset/__init__.py
scarches/dataset/trvae/__init__.py
scarches/dataset/trvae/_utils.py
scarches/dataset/trvae/anndata.py
scarches/dataset/trvae/data_handling.py
scarches/metrics/__init__.py
scarches/metrics/clustering.py
scarches/metrics/metrics.py
scarches/models/__init__.py
scarches/models/trvae/__init__.py
scarches/models/trvae/_utils.py
scarches/models/trvae/activations.py
scarches/models/trvae/losses.py
scarches/models/trvae/modules.py
scarches/models/trvae/trvae.py
scarches/models/trvae/trvae_model.py
scarches/plotting/__init__.py
scarches/plotting/_alluvial.py
scarches/plotting/sankey.py
scarches/plotting/scvi_eval.py
scarches/plotting/trvae_eval.py
scarches/surgery/__init__.py
scarches/surgery/scvi.py
scarches/surgery/trvae.py
scarches/trainers/__init__.py
scarches/trainers/scvi/__init__.py
scarches/trainers/scvi/trainers.py
scarches/trainers/trvae/__init__.py
scarches/trainers/trvae/_utils.py
scarches/trainers/trvae/trainer.py
scarches/trainers/trvae/unsupervised.py
scarches/utils/__init__.py
scarches/utils/monitor.py
scarches/utils/scvi/__init__.py
scarches/utils/scvi/_constants.py
scarches/utils/scvi/_settings.py
scarches/zenodo/__init__.py
scarches/zenodo/deposition.py
scarches/zenodo/file.py
scarches/zenodo/zip.py
tests/scvi_tests/scanvi_surgery.py
tests/trvae_tests/batch_loading_test.py
tests/trvae_tests/trvae_test.py