├── .gitignore ├── Dockerfile ├── README.md ├── config ├── sing_emb.yaml └── sing_emb_mgraph.yaml └── scripts ├── additional_network_functions.r ├── download_data.r ├── foxc12 ├── chimeras_compare_frequency.r ├── control_chim_timing.r ├── definition_cell_types_endoderm_ectoderm_embryonic_mesoderm.r ├── differential_expression_analysis.r ├── foxc_chim_timing.r ├── generate_chimera_tetraploid_data_analysis.r ├── preprocessing │ ├── foxc_control_gating.r │ ├── foxc_control_remove_exe_ectoderm_and_parietal_endo_cls.r │ ├── foxc_control_split_into_experiment_type.r │ ├── merge_umi_mat_with_wt10_umi_mat.r │ └── summary_preprocessing.r ├── transfer_cell_type_annotation.r └── transfer_time_annotation.r ├── generate_mc_mgraph_network ├── annot_mc_by_flows.r ├── gen_mc.r ├── gen_mc2d_umap.r ├── gen_mgraph.r ├── gen_network.r └── generic_mc.r ├── generate_paper_figures ├── fig_1.r ├── fig_2.r ├── fig_3.r ├── fig_4.r ├── fig_5.r ├── fig_6.r ├── fig_7.r ├── fig_s1.r ├── fig_s2.r ├── fig_s3.r ├── fig_s4.r ├── fig_s5.r ├── fig_s6.r ├── fig_s7.r ├── generate_all_figures.r ├── plot_3d_vein.r ├── plot_network.r └── plot_vein.r ├── initialize_scripts.r ├── parameter_stability_analysis.r ├── single_embryo_timing.r └── test_cmp_network_flow_model.r /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tanaylab/embflow/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tanaylab/embflow/HEAD/Dockerfile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tanaylab/embflow/HEAD/README.md -------------------------------------------------------------------------------- /config/sing_emb.yaml: 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