Man pages for dynwrap
Representing and Inferring Single-Cell Trajectories
| add_attraction | Add attraction of cells using RNA velocity |
| add_branch_trajectory | Construct a trajectory given its branch network and the... |
| add_cell_graph | Constructs a trajectory using a graph between cells, by... |
| add_cell_waypoints | Add or select waypoint cells of a trajectory |
| add_cluster_graph | Constructs a trajectory using a cell grouping and a network... |
| add_cyclic_trajectory | Constructs a circular trajectory using the pseudotime values... |
| add_dimred | Add or create a dimensionality reduction |
| add_dimred_projection | Constructs a trajectory by projecting cells within a... |
| add_end_state_probabilities | Constructs a multifurcating trajectory using end state... |
| add_expression | Add count and normalised expression values to a dataset |
| add_feature_importance | Add a feature importance to a dataset |
| add_grouping | Add a cell grouping to a dataset |
| add_linear_trajectory | Constructs a linear trajectory using pseudotime values |
| add_prior_information | Add or compute prior information for a trajectory |
| add_pseudotime | Add or calculate pseudotime as distance from the root |
| add_regulatory_network | Add a GRN to a dynwrap object |
| add_root | Root the trajectory |
| add_tde_overall | Add information on overall differentially expressed features |
| add_timings | Add timings to a trajectory |
| add_trajectory | Construct a trajectory given its milestone network and... |
| add_waypoints | Add or create waypoints to a trajectory |
| allowed_inputs | All allowed inputs for a TI method |
| allowed_outputs | All allowed outputs for a TI method |
| calculate_attraction | Calculate the attraction of cells to other cells using... |
| calculate_average | Calculate average values of a matrix |
| calculate_geodesic_distances | Calculate geodesic distances between cells in a trajectory |
| calculate_trajectory_dimred | Layout the trajectory and its cells in 2 dimensions using a... |
| classify_milestone_network | Classify a milestone network |
| common_param | Common param |
| convert_definition | Convert a definition loaded in from a yaml |
| convert_milestone_percentages_to_progressions | Conversion between milestone percentages and progressions |
| convert_progressions_to_milestone_percentages | Conversion between milestone percentages and progressions |
| create_ti_method_container | Create a TI method from a docker / singularity container |
| create_ti_method_definition | Create a TI method from a local method definition file |
| create_ti_method_r | Create a TI method from an R function wrapper |
| def_author | Meta information on an author |
| def_container | Meta information on the container in which the wrapper... |
| definition | Create a definition |
| def_manuscript | Meta information on the manuscript |
| def_method | Define meta information on the TI method. |
| def_package | Meta information on the package in which the TI function... |
| def_parameters | Meta information on the parameters of the TI method |
| def_wrapper | Meta information on the wrapper |
| dot-method_process_definition | Method process definition |
| dynwrap | Inferring and adapting single-cell trajectories |
| example_dataset | Example dataset |
| example_trajectory | Example trajectory |
| flip_edges | Flip a set of edges of the milestone network |
| gather_cells_at_milestones | Gather cells to their closest milestones |
| generate_parameter_documentation | Generate the parameter documentation of a method, use with... |
| get_default_parameters | Get the default parameters of a method |
| get_ti_methods | Return all TI that are installed in one or more packages |
| group_from_trajectory | Create a grouping from a trajectory |
| infer_trajectories | Infer one or more trajectories from a single-cell dataset |
| label_milestones | Label milestones either manually ('label_milestones') or... |
| priors | Metadata on priors |
| prior_usages | Metadata on prior usages |
| project_trajectory | Project a trajectory onto a dimensionality reduction |
| project_waypoints | Project waypoints of a trajectory (e.g. milestones) into a... |
| random_seed | Generate a random seed |
| reexports | Objects exported from other packages |
| simplify_igraph_network | Simplify an igraph network such that consecutive linear edges... |
| simplify_trajectory | Simplify a trajectory by removing transient milestones |
| trajectory_type_dag | A DAG connecting different trajectory types |
| trajectory_types | Metadata on the trajectory types |
| wrap_data | A data wrapper for datasets and trajectories |
| wrap_expression | Create a wrapper object with expression and counts |
| wrapper_types | Metadata on wrapper types |
