├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── adapt_orient_topology.R ├── add_regulatory_network.R ├── calculate_average.R ├── calculate_geodesic_distances.R ├── calculate_trajectory_dimred.R ├── classify_milestone_network.R ├── container_get.R ├── convert_milestone_percentages_to_progressions.R ├── convert_progressions_to_milestone_percentages.R ├── data.R ├── method_create_ti_method_container.R ├── method_create_ti_method_definition.R ├── method_create_ti_method_r.R ├── method_execute.R ├── method_extract_args.R ├── method_get_ti_methods.R ├── method_infer_trajectory.R ├── method_process_definition.R ├── package.R ├── project_waypoints.R ├── reexport.R ├── simplify_igraph_network.R ├── simplify_trajectory.R ├── wrap_add_attraction.R ├── wrap_add_branch_trajectory.R ├── wrap_add_cell_graph.R ├── wrap_add_cell_waypoints.R ├── wrap_add_cluster_graph.R ├── wrap_add_cyclic_trajectory.R ├── wrap_add_dimred.R ├── wrap_add_dimred_projection.R ├── wrap_add_end_state_probabilities.R ├── wrap_add_expression.R ├── wrap_add_feature_importance.R ├── wrap_add_grouping.R ├── wrap_add_linear_trajectory.R ├── wrap_add_prior_information.R ├── wrap_add_pseudotime.R ├── wrap_add_root.R ├── wrap_add_tde_overall.R ├── wrap_add_timings.R ├── wrap_add_trajectory.R ├── wrap_add_waypoints.R ├── wrap_data.R ├── wrap_gather_cells_at_milestones.R └── wrap_label_milestones.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── cran-comments.md ├── data-raw ├── allowed_inputs_outputs.R ├── example_dataset.R ├── priors.R ├── trajectory_types.R └── wrapper_types.R ├── data ├── allowed_inputs.rda ├── allowed_outputs.rda ├── example_dataset.rda ├── example_trajectory.rda ├── prior_usages.rda ├── priors.rda ├── trajectory_type_dag.rda ├── trajectory_types.rda └── wrapper_types.rda ├── dynwrap.Rproj ├── inst ├── CITATION ├── examples │ ├── docker │ │ ├── Dockerfile │ │ ├── definition.yml │ │ └── run.py │ └── script │ │ ├── definition.yml │ │ ├── run.R │ │ └── run.py └── tests │ └── testthat │ ├── helper-ti_comp1.R │ ├── helper-ti_error.R │ ├── helper-ti_identity.R │ ├── helper-ti_random.R │ └── helper-ti_shuffle.R ├── man ├── add_attraction.Rd ├── add_branch_trajectory.Rd ├── add_cell_graph.Rd ├── add_cell_waypoints.Rd ├── add_cluster_graph.Rd ├── add_cyclic_trajectory.Rd ├── add_dimred.Rd ├── add_dimred_projection.Rd ├── add_end_state_probabilities.Rd ├── add_expression.Rd ├── add_feature_importance.Rd ├── add_grouping.Rd ├── add_linear_trajectory.Rd ├── add_prior_information.Rd ├── add_pseudotime.Rd ├── add_regulatory_network.Rd ├── add_root.Rd ├── add_tde_overall.Rd ├── add_timings.Rd ├── add_trajectory.Rd ├── add_waypoints.Rd ├── allowed_inputs.Rd ├── allowed_outputs.Rd ├── calculate_attraction.Rd ├── calculate_average.Rd ├── calculate_geodesic_distances.Rd ├── calculate_trajectory_dimred.Rd ├── classify_milestone_network.Rd ├── common_param.Rd ├── convert_definition.Rd ├── convert_milestone_percentages_to_progressions.Rd ├── convert_progressions_to_milestone_percentages.Rd ├── create_ti_method_container.Rd ├── create_ti_method_definition.Rd ├── create_ti_method_r.Rd ├── def_author.Rd ├── def_container.Rd ├── def_manuscript.Rd ├── def_method.Rd ├── def_package.Rd ├── def_parameters.Rd ├── def_wrapper.Rd ├── definition.Rd ├── dot-method_process_definition.Rd ├── dynwrap.Rd ├── example_dataset.Rd ├── example_trajectory.Rd ├── figures │ ├── dependencies.png │ ├── logo.png │ ├── logo.svg │ ├── overview_wrapping_v3.png │ └── trajectory_model.png ├── flip_edges.Rd ├── gather_cells_at_milestones.Rd ├── generate_parameter_documentation.Rd ├── get_default_parameters.Rd ├── get_ti_methods.Rd ├── group_from_trajectory.Rd ├── infer_trajectories.Rd ├── label_milestones.Rd ├── prior_usages.Rd ├── priors.Rd ├── project_trajectory.Rd ├── project_waypoints.Rd ├── random_seed.Rd ├── reexports.Rd ├── simplify_igraph_network.Rd ├── simplify_trajectory.Rd ├── trajectory_type_dag.Rd ├── trajectory_types.Rd ├── wrap_data.Rd ├── wrap_expression.Rd └── wrapper_types.Rd ├── revdep ├── .gitignore ├── README.md ├── cran.md ├── email.yml ├── failures.md └── problems.md ├── tests ├── testthat.R └── testthat │ ├── nothelper-methods.R │ ├── test-adapt_orient_topology.R │ ├── test-calculate_average.R │ ├── test-calculate_geodesic_distances.R │ ├── test-calculate_trajectory_dimred.R │ ├── test-classify_milestone_network.R │ ├── test-method_create_ti_method_container.R │ ├── test-method_create_ti_method_r.R │ ├── test-method_infer_trajectory.R │ ├── test-method_parse_parameter_definition.R │ ├── test-milestone_convertors.R │ ├── test-simplify_igraph_network.R │ ├── test-simplify_trajectory.R │ ├── test-wrap_add_branch_trajectory.R │ ├── test-wrap_add_cell_graph.R │ ├── test-wrap_add_cell_waypoints.R │ ├── test-wrap_add_cyclic_trajectory.R │ ├── 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