.method_process_definition
                        Method process definition
add_attraction          Add attraction of cells using RNA velocity
add_branch_trajectory   Construct a trajectory given its branch network
                        and the pseudotime of the cells on one of the
                        branches.
add_cell_graph          Constructs a trajectory using a graph between
                        cells, by mapping cells onto a set of backbone
                        cells.
add_cell_waypoints      Add or select waypoint cells of a trajectory
add_cluster_graph       Constructs a trajectory using a cell grouping
                        and a network between groups. Will use an
                        existing grouping if it is present in the
                        dataset.
add_cyclic_trajectory   Constructs a circular trajectory using the
                        pseudotime values of each cell.
add_dimred              Add or create a dimensionality reduction
add_dimred_projection   Constructs a trajectory by projecting cells
                        within a dimensionality reduction
add_end_state_probabilities
                        Constructs a multifurcating trajectory using
                        end state probabilities
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_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 milestone percentages or
                        progressions
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 velocity
calculate_average_by_group
                        Calculate average values of a matrix
calculate_geodesic_distances
                        Calculate geodesic distances between cells in a
                        trajectory
calculate_pseudotime    Add or calculate pseudotime as distance from
                        the root
calculate_trajectory_dimred
                        Layout the trajectory and its cells in 2
                        dimensions using a graph layout
classify_milestone_network
                        Classify a milestone network
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 resides
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 resides
def_parameters          Meta information on the parameters of the TI
                        method
def_wrapper             Meta information on the wrapper
definition              Create a definition
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 @eval
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 using marker genes
                        ('label_milestones_markers')
prior_usages            Metadata on prior usages
priors                  Metadata on priors
project_trajectory      Project a trajectory onto a dimensionality
                        reduction
project_waypoints       Project waypoints of a trajectory (e.g.
                        milestones) into a space defined by cells (e.g.
                        expression or a dimensionality reduction)
random_seed             Generate a random seed
select_waypoints        Add or create waypoints to a trajectory
simplify_igraph_network
                        Simplify an igraph network such that
                        consecutive linear edges are removed
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
