LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
documentation/INSTALL.md
documentation/OUTPUTS.md
documentation/QUICKSTART.md
documentation/USAGE.md
examples/README.md
examples/celios_run_example.py
examples/celios_run_tissue_example.py
examples/config.yaml
examples/config_tissue.yaml
src/celios/__init__.py
src/celios/base_defaults.py
src/celios/cli.py
src/celios/core.py
src/celios/features/__init__.py
src/celios/features/activity_parser.py
src/celios/features/binary_builder.py
src/celios/features/binary_parser.py
src/celios/features/cline.py
src/celios/features/expression_builder.py
src/celios/features/files.py
src/celios/features/master_matrix.py
src/celios/features/node.py
src/celios/features/node_mapping.py
src/celios/features/sifbase.py
src/celios/features/source_selector.py
src/celios/features/tf_builder.py
src/celios/features/tissue.py
src/celios/features/training.py
src/celios/utils/__init__.py
src/celios/utils/cell_line_resolver.py
src/celios/utils/id_normalization.py
src/celios/utils/io.py
src/celios/utils/report.py
src/celios/utils/validate.py