.gitignore
.pre-commit-config.yaml
CITATION.cff
CONTRIBUTING.md
LICENSE
README.md
buddi_goal.png
environment.yml
pyproject.toml
uv.lock
.github/dependabot.yml
.github/workflows/docs.yml
.github/workflows/gh-release-drafts.yml
.github/workflows/pypi.yml
.github/workflows/tests.yml
docs/src/conf.py
docs/src/index.md
docs/src/python-api.md
examples/1.prepare_pseudobulk.ipynb
examples/2.format_bulk.ipynb
examples/3.legacy_prepare_train_data.ipynb
examples/4.legacy_train_buddi4.ipynb
examples/example_buddi3/1.prepare_buddi3_train_data.ipynb
examples/example_buddi3/2.train_buddi3.ipynb
examples/example_buddi4/1.prepare_buddi4_train_data.ipynb
examples/example_buddi4/2b.train_buddi4_class.ipynb
examples/example_data/bulk_data/GSE132040_190214.csv.gz
examples/example_data/bulk_data/GSE132040_MACA_Bulk_metadata.csv
examples/example_data/bulk_data/liver_bulk_processed.h5ad
examples/example_data/cibersort_liver/CIBERSORTx_Job20_all-liver_0_cybersort_sig_inferred_phenoclasses.CIBERSORTx_Job20_all-liver_0_cybersort_sig_inferred_refsample.bm.K999.txt
examples/example_data/preprocessed_data/.gitkeep
examples/example_data/preprocessed_data/README.md
examples/example_data/processed_sc_liver/liver_droplet_processed.h5ad
src/buddi/README.md
src/buddi/__init__.py
src/buddi/_version.py
src/buddi.egg-info/PKG-INFO
src/buddi.egg-info/SOURCES.txt
src/buddi.egg-info/dependency_links.txt
src/buddi.egg-info/requires.txt
src/buddi.egg-info/top_level.txt
src/buddi/data/BuDDINData.py
src/buddi/data/README.md
src/buddi/data/__init__.py
src/buddi/data/buddi4data.py
src/buddi/dataset/README.md
src/buddi/dataset/__init__.py
src/buddi/dataset/buddi3_dataset.py
src/buddi/dataset/buddi4_dataset.py
src/buddi/dataset/data_split.py
src/buddi/dataset/dataset_generator.py
src/buddi/models/README.md
src/buddi/models/__init__.py
src/buddi/models/buddi3_class.py
src/buddi/models/buddi4.py
src/buddi/models/buddi4_class.py
src/buddi/models/buddi_abstract_class.py
src/buddi/models/fit.py
src/buddi/models/components/__init__.py
src/buddi/models/components/branches.py
src/buddi/models/components/layers.py
src/buddi/models/components/losses.py
src/buddi/models/components/wrapped_branches.py
src/buddi/plotting/__init__.py
src/buddi/plotting/plot_data.py
src/buddi/plotting/plot_latent_space.py
src/buddi/plotting/plot_loss.py
src/buddi/preprocessing/README.md
src/buddi/preprocessing/__init__.py
src/buddi/preprocessing/generate_pseudo_bulks.py
src/buddi/preprocessing/sc_augmentor.py
src/buddi/preprocessing/utils.py
tests/__init__.py
tests/conftest.py
tests/test_notebooks.py