CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
data/test/README.md
data/test/control_genes.json
data/test/genes.txt
data/test/sim_adata.h5ad
docs/README.md
docs/methods.md
docs/output_structure.md
scDCF/__init__.py
scDCF/__main__.py
scDCF/analysis.py
scDCF/cell_metadata.py
scDCF/control_genes.py
scDCF/dependencies.py
scDCF/main.py
scDCF/parallel.py
scDCF/post_analysis.py
scDCF/trait_association.py
scDCF/utils.py
scdcf.egg-info/PKG-INFO
scdcf.egg-info/SOURCES.txt
scdcf.egg-info/dependency_links.txt
scdcf.egg-info/entry_points.txt
scdcf.egg-info/requires.txt
scdcf.egg-info/top_level.txt
tests/test_organization.py
tests/test_pipeline_smoke.py