Files in dynwrap

Representing and Inferring Single-Cell Trajectories

NEWS.md README.md R/method_create_ti_method_definition.R R/wrap_add_linear_trajectory.R R/wrap_data.R R/wrap_add_cyclic_trajectory.R R/method_create_ti_method_container.R R/adapt_orient_topology.R R/add_regulatory_network.R R/method_infer_trajectory.R R/calculate_geodesic_distances.R R/method_process_definition.R R/wrap_add_expression.R R/simplify_trajectory.R R/calculate_average.R R/wrap_add_cluster_graph.R R/wrap_gather_cells_at_milestones.R R/simplify_igraph_network.R R/convert_progressions_to_milestone_percentages.R R/method_extract_args.R R/project_waypoints.R R/wrap_add_dimred_projection.R R/wrap_add_waypoints.R R/data.R R/wrap_add_cell_waypoints.R R/wrap_add_grouping.R R/wrap_add_branch_trajectory.R R/wrap_add_prior_information.R R/wrap_add_tde_overall.R R/method_get_ti_methods.R R/classify_milestone_network.R R/wrap_label_milestones.R R/convert_milestone_percentages_to_progressions.R R/method_execute.R R/package.R R/wrap_add_trajectory.R R/method_create_ti_method_r.R R/wrap_add_cell_graph.R R/container_get.R R/wrap_add_feature_importance.R R/wrap_add_attraction.R R/calculate_trajectory_dimred.R R/wrap_add_pseudotime.R R/wrap_add_end_state_probabilities.R R/wrap_add_root.R R/reexport.R R/wrap_add_timings.R R/wrap_add_dimred.R inst/doc/create_ti_method_r.Rmd inst/doc/create_ti_method_wrappers.Rmd inst/doc/create_ti_method_definition.Rmd inst/doc/create_ti_method_container.R inst/doc/create_ti_method_container.Rmd inst/doc/create_ti_method_wrappers.R inst/doc/create_ti_method_r.R inst/doc/create_ti_method_definition.R inst/examples/script/run.R inst/tests/testthat/helper-ti_error.R inst/tests/testthat/helper-ti_random.R inst/tests/testthat/helper-ti_identity.R inst/tests/testthat/helper-ti_shuffle.R inst/tests/testthat/helper-ti_comp1.R tests/testthat.R tests/testthat/test-wrap_add_expression.R tests/testthat/test-wrap_cell_group.R tests/testthat/test-method_parse_parameter_definition.R tests/testthat/test-wrap_add_branch_trajectory.R tests/testthat/test-wrap_add_trajectory.R tests/testthat/nothelper-methods.R tests/testthat/test-method_infer_trajectory.R tests/testthat/test-classify_milestone_network.R tests/testthat/test-wrap_add_root_and_add_pseudotime.R tests/testthat/test-wrap_add_timings.R tests/testthat/test-wrap_cluster_graph.R tests/testthat/test-method_create_ti_method_r.R tests/testthat/test-method_create_ti_method_container.R tests/testthat/test-wrap_add_cell_waypoints.R tests/testthat/test-wrap_add_end_state_probabilities.R tests/testthat/test-wrap_add_cyclic_trajectory.R tests/testthat/test-wrap_add_dimred.R tests/testthat/test-wrap_add_waypoints.R tests/testthat/test-wrap_add_dimred_projection.R tests/testthat/test-wrap_label_milestones.R tests/testthat/test-calculate_trajectory_dimred.R tests/testthat/test-wrap_add_cell_graph.R tests/testthat/test-adapt_orient_topology.R tests/testthat/test-calculate_average.R tests/testthat/test-wrap_data.R tests/testthat/test-wrap_add_linear_trajectory.R tests/testthat/test-wrap_add_grouping.R tests/testthat/test-simplify_trajectory.R tests/testthat/test-simplify_igraph_network.R tests/testthat/test-wrap_add_prior_information.R tests/testthat/test-calculate_geodesic_distances.R tests/testthat/test-wrap_add_pseudotime.R tests/testthat/test-milestone_convertors.R vignettes/create_ti_method_r.Rmd vignettes/create_ti_method_wrappers.Rmd vignettes/create_ti_method_definition.Rmd vignettes/create_ti_method_container.Rmd man/trajectory_type_dag.Rd man/add_regulatory_network.Rd man/project_trajectory.Rd man/def_container.Rd man/generate_parameter_documentation.Rd man/flip_edges.Rd man/definition.Rd man/reexports.Rd man/def_wrapper.Rd man/prior_usages.Rd man/add_dimred_projection.Rd man/add_timings.Rd man/def_author.Rd man/convert_milestone_percentages_to_progressions.Rd man/gather_cells_at_milestones.Rd man/add_linear_trajectory.Rd man/dot-method_process_definition.Rd man/calculate_trajectory_dimred.Rd man/add_expression.Rd man/add_root.Rd man/get_default_parameters.Rd man/example_trajectory.Rd man/priors.Rd man/trajectory_types.Rd man/classify_milestone_network.Rd man/add_prior_information.Rd man/add_branch_trajectory.Rd man/common_param.Rd man/allowed_inputs.Rd man/wrapper_types.Rd man/wrap_expression.Rd man/def_manuscript.Rd man/def_package.Rd man/def_method.Rd man/random_seed.Rd man/allowed_outputs.Rd man/get_ti_methods.Rd man/create_ti_method_container.Rd man/add_feature_importance.Rd man/def_parameters.Rd man/add_tde_overall.Rd man/add_end_state_probabilities.Rd man/add_waypoints.Rd man/add_grouping.Rd man/add_attraction.Rd man/add_cell_graph.Rd man/simplify_igraph_network.Rd man/convert_definition.Rd man/calculate_attraction.Rd man/calculate_geodesic_distances.Rd man/add_cyclic_trajectory.Rd man/add_pseudotime.Rd man/infer_trajectories.Rd man/create_ti_method_definition.Rd man/dynwrap.Rd man/add_cluster_graph.Rd man/add_trajectory.Rd man/convert_progressions_to_milestone_percentages.Rd man/add_dimred.Rd man/project_waypoints.Rd man/wrap_data.Rd man/simplify_trajectory.Rd man/example_dataset.Rd man/label_milestones.Rd man/group_from_trajectory.Rd man/calculate_average.Rd man/create_ti_method_r.Rd man/add_cell_waypoints.Rd