.gitignore
.readthedocs.yml
.travis.yml
LICENSE
README.rst
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
docs/api/zenodo.rst
notebooks/SageNet_mouse_embryo.ipynb
notebooks/expimap_surgery_pipeline_advanced.ipynb
notebooks/expimap_surgery_pipeline_basic.ipynb
notebooks/multigrate.ipynb
notebooks/mvTCR_borcherding.ipynb
notebooks/reference_building_from_scratch.ipynb
notebooks/scanvi_surgery_pipeline.ipynb
notebooks/scgen_map_query.ipynb
notebooks/scpoli_surgery_pipeline.ipynb
notebooks/scvi_surgery_pipeline.ipynb
notebooks/totalvi_surgery_pipeline.ipynb
notebooks/trVAE_zenodo_pipeline.ipynb
notebooks/treeArches_identifying_new_ct.ipynb
notebooks/treeArches_pbmc.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/classifiers/__init__.py
scarches/dataset/__init__.py
scarches/dataset/DHH_data/_DHH_data.py
scarches/dataset/DHH_data/__init__.py
scarches/dataset/MGA_data/_MGA_data.py
scarches/dataset/MGA_data/__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/base/__init__.py
scarches/models/base/_base.py
scarches/models/base/_utils.py
scarches/models/expimap/__init__.py
scarches/models/expimap/expimap.py
scarches/models/expimap/expimap_model.py
scarches/models/expimap/losses.py
scarches/models/expimap/modules.py
scarches/models/sagenet/__init__.py
scarches/models/sagenet/classifier.py
scarches/models/sagenet/model.py
scarches/models/sagenet/sagenet.py
scarches/models/sagenet/utils.py
scarches/models/scgen/__init__.py
scarches/models/scgen/_utils.py
scarches/models/scgen/modules.py
scarches/models/scgen/vaearith.py
scarches/models/scgen/vaearith_model.py
scarches/models/scpoli/__init__.py
scarches/models/scpoli/scpoli.py
scarches/models/scpoli/scpoli_model.py
scarches/models/trvae/__init__.py
scarches/models/trvae/_utils.py
scarches/models/trvae/adaptors.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/terms_scores.py
scarches/plotting/trvae_eval.py
scarches/surgery/__init__.py
scarches/surgery/trvae.py
scarches/trainers/__init__.py
scarches/trainers/expimap/__init__.py
scarches/trainers/expimap/regularized.py
scarches/trainers/scgen/__init__.py
scarches/trainers/scgen/_utils.py
scarches/trainers/scgen/trainer.py
scarches/trainers/scpoli/__init__.py
scarches/trainers/scpoli/_utils.py
scarches/trainers/scpoli/trainer.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/annotations.py
scarches/utils/monitor.py
scarches/zenodo/__init__.py
scarches/zenodo/deposition.py
scarches/zenodo/file.py
scarches/zenodo/zip.py
tests/test_dataloader.py