├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── datasets ├── ATAC │ └── README.md ├── GeneInformation │ ├── .gitignore │ └── download.sh ├── KEGG │ ├── .gitignore │ └── README.md ├── Paul15 │ └── INFO.md ├── README.md ├── RealNet │ ├── .gitignore │ └── download.sh ├── RegNet │ ├── .gitignore │ └── download.sh ├── RegulonDB │ ├── .gitignore │ └── download.sh ├── STRING │ ├── .gitignore │ └── download.sh └── SarsCov2 │ └── INFO.md ├── docs ├── cell_population.md ├── data │ ├── composite_graphs.md │ ├── gene_regulatory_networks.md │ ├── interaction_data.md │ ├── pathways.md │ ├── protein_interactions.md │ ├── random_graphs.md │ └── utils.md ├── figure1.png ├── flecs_logo.png ├── index.md ├── intervention.md ├── mutation.md ├── sets.md ├── trajectory.md └── utils.md ├── environment_cpu.yml ├── environment_gpu.yml ├── figure2 ├── CellPaths.ipynb ├── CellPathsMethods.ipynb ├── EnsembleInterventional.ipynb ├── Evaluation.ipynb ├── Genie3.ipynb ├── PantherDBanalysis.ipynb ├── Paul15Preprocessing.ipynb ├── Prettytable.ipynb ├── VelocityConfidenceEvaluation.ipynb ├── genie3_grn_script.py ├── genie3_script.py ├── scTour_inference.ipynb ├── torchCFM.ipynb ├── train_ensemble_gene.py ├── train_ensemble_gene_ko_cebpa.py ├── train_ensemble_gene_ko_cebpe.py ├── train_gene.py ├── train_gene_ko_cebpa.py ├── train_gene_ko_cebpe.py ├── train_gene_latent.py └── train_gene_protein.py ├── figure4 ├── EvaluationReplogle.ipynb ├── Genie3.ipynb ├── PantherDBanalysis.ipynb ├── ReplogleDPTCellPathsWithKO.ipynb ├── ReplogleEnsembleInterventional.ipynb ├── ReploglePreprocessing.ipynb ├── SubgraphDrawing.ipynb ├── data │ ├── INFO.md │ └── regev_lab_cell_cycle_genes.txt ├── genie3_grn_script.py ├── genie3_script.py ├── train_ensemble_replogle.py ├── train_ensemble_replogle_all_ko.py └── train_replogle.py ├── figure5 ├── EvaluationInterventionalSciplex3.ipynb ├── EvaluationSciplex3.ipynb ├── PantherDBanalysis.ipynb ├── ScGen.ipynb ├── SciplexDPTCellPathsWithKO.ipynb ├── SciplexPreprocessing.ipynb ├── sciplex_in_sample_indices.npy ├── sciplex_out_sample_indices.npy ├── train_dataset_pert_paths.npy ├── train_interventional_sciplex.py ├── train_sciplex.py └── train_sciplex_flow_matching.py ├── flecs ├── __init__.py ├── cell_population.py ├── data │ ├── __init__.py │ ├── composite_graphs.py │ ├── gene_regulatory_networks.py │ ├── interaction_data.py │ ├── pathways.py │ ├── protein_interactions.py │ ├── random_graphs.py │ └── utils.py ├── decay.py ├── intervention.py ├── mutation.py ├── production.py ├── sc │ ├── dataset.py │ ├── model.py │ └── utils.py ├── sets.py ├── trajectory.py └── utils.py ├── mkdocs.yml ├── notebooks ├── Interaction Databases.ipynb ├── Overview.ipynb ├── SingleCellExample.ipynb └── Tutorial.ipynb ├── pyproject.toml └── tests ├── test_basic.py ├── test_cell_population.py ├── test_data.py ├── test_decay.py ├── test_intervention.py ├── test_mutation.py ├── test_production.py ├── test_sets.py ├── 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