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.gitignore
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LICENSE
README.md
codecov.yml
pyproject.toml
readthedocs.yml
.github/workflows/release.yml
.github/workflows/test.yml
docs/Makefile
docs/conf.py
docs/index.md
docs/make.bat
docs/references.bib
docs/references.md
docs/_static/img/overview_fig.png
docs/_static/img/perturbation_overview_fig.png
docs/_templates/class_no_inherited.rst
docs/_templates/autosummary/class.rst
docs/about/index.rst
docs/api/.Rhistory
docs/api/datasets.md
docs/api/index.md
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docs/api/model.md
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docs/api/preprocessing.md
docs/api/tools.md
docs/extensions/typed_returns.py
docs/model/index.rst
docs/release_notes/index.rst
docs/release_notes/v0.1.0.rst
docs/tutorials/index.md
docs/tutorials/index_hindbrain.md
docs/tutorials/index_humanlimb.md
docs/tutorials/index_modelcomp.md
docs/tutorials/index_murine.md
docs/tutorials/index_schwann.md
docs/tutorials/index_zebrafish.md
docs/tutorials/hindbrain/modelcomparison.ipynb
docs/tutorials/hindbrain/preprocessing.ipynb
docs/tutorials/humanlimb/Limb_ModelComp.ipynb
docs/tutorials/modelcomparison/ModelComp.ipynb
docs/tutorials/murine/01_SCENIC_tutorial.ipynb
docs/tutorials/murine/02_RegVelo_preparation.ipynb
docs/tutorials/murine/03_perturbation_tutorial_murine.ipynb
docs/tutorials/schwann/modelcomparison.ipynb
docs/tutorials/zebrafish/grn_tutorial.ipynb
docs/tutorials/zebrafish/tutorial.ipynb
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src/regvelo/ModelComparison.py
src/regvelo/__init__.py
src/regvelo/_constants.py
src/regvelo/_model.py
src/regvelo/_module.py
src/regvelo.egg-info/PKG-INFO
src/regvelo.egg-info/SOURCES.txt
src/regvelo.egg-info/dependency_links.txt
src/regvelo.egg-info/requires.txt
src/regvelo.egg-info/top_level.txt
src/regvelo/datasets/__init__.py
src/regvelo/datasets/_datasets.py
src/regvelo/metrics/__init__.py
src/regvelo/metrics/_abundance_test.py
src/regvelo/metrics/_cellfate_perturbation.py
src/regvelo/metrics/_depletion_score.py
src/regvelo/metrics/_tsi.py
src/regvelo/metrics/_utils.py
src/regvelo/plotting/__init__.py
src/regvelo/plotting/_cellfate_perturbation.py
src/regvelo/plotting/_commitment_score.py
src/regvelo/plotting/_depletion_score.py
src/regvelo/plotting/_regulatory_network.py
src/regvelo/plotting/_simulated_visit_diff.py
src/regvelo/plotting/_utils.py
src/regvelo/preprocessing/__init__.py
src/regvelo/preprocessing/_filter_genes.py
src/regvelo/preprocessing/_preprocess_data.py
src/regvelo/preprocessing/_sanity_check.py
src/regvelo/preprocessing/_set_prior_grn.py
src/regvelo/tools/_TFScanning_func.py
src/regvelo/tools/_TFscreening.py
src/regvelo/tools/__init__.py
src/regvelo/tools/_in_silico_block_regulation_simulation.py
src/regvelo/tools/_in_silico_block_simulation.py
src/regvelo/tools/_inferred_grn.py
src/regvelo/tools/_markov_density_simulation.py
src/regvelo/tools/_perturbation_effect.py
src/regvelo/tools/_regulation_scanning.py
src/regvelo/tools/_set_output.py
src/regvelo/tools/_simulated_visit_diff.py
src/regvelo/tools/_utils.py
tests/__init__.py
tests/test_regvelo.py