.method_process_definition	dot-method_process_definition
add_attraction	add_attraction
add_branch_trajectory	add_branch_trajectory
add_cell_graph	add_cell_graph
add_cell_waypoints	add_cell_waypoints
add_cluster_graph	add_cluster_graph
add_cyclic_trajectory	add_cyclic_trajectory
add_dimred	add_dimred
add_dimred_projection	add_dimred_projection
add_end_state_probabilities	add_end_state_probabilities
add_expression	add_expression
add_feature_importance	add_feature_importance
add_grouping	add_grouping
add_linear_trajectory	add_linear_trajectory
add_prior_information	add_prior_information
add_pseudotime	add_pseudotime
add_regulatory_network	add_regulatory_network
add_root	add_root
add_root_using_expression	add_root
add_tde_overall	add_tde_overall
add_timings	add_timings
add_timing_checkpoint	add_timings
add_trajectory	add_trajectory
add_waypoints	add_waypoints
allowed_inputs	allowed_inputs
allowed_outputs	allowed_outputs
calculate_attraction	calculate_attraction
calculate_average_by_group	calculate_average
calculate_geodesic_distances	calculate_geodesic_distances
calculate_pseudotime	add_pseudotime
calculate_trajectory_dimred	calculate_trajectory_dimred
classify_milestone_network	classify_milestone_network
common_param	common_param
compute_tented_geodesic_distances	calculate_geodesic_distances
convert_definition	convert_definition
convert_milestone_percentages_to_progressions	convert_milestone_percentages_to_progressions
convert_progressions_to_milestone_percentages	convert_progressions_to_milestone_percentages
create_config	reexports
create_docker_config	reexports
create_singularity_config	reexports
create_ti_method_container	create_ti_method_container
create_ti_method_definition	create_ti_method_definition
create_ti_method_r	create_ti_method_r
definition	definition
def_author	def_author
def_container	def_container
def_manuscript	def_manuscript
def_method	def_method
def_package	def_package
def_parameters	def_parameters
def_wrapper	def_wrapper
determine_cell_trajectory_positions	add_cell_waypoints
dynwrap	dynwrap
example_dataset	example_dataset
example_trajectory	example_trajectory
flip_edges	flip_edges
gather_cells_at_milestones	gather_cells_at_milestones
generate_parameter_documentation	generate_parameter_documentation
generate_prior_information	add_prior_information
get_default_config	reexports
get_default_parameters	get_default_parameters
get_dimred	add_dimred
get_expression	add_expression
get_grouping	add_grouping
get_milestone_labelling	label_milestones
get_ti_methods	get_ti_methods
group_from_trajectory	group_from_trajectory
group_onto_nearest_milestones	group_from_trajectory
group_onto_trajectory_edges	group_from_trajectory
infer_trajectories	infer_trajectories
infer_trajectory	infer_trajectories
is_data_wrapper	wrap_data
is_rooted	add_root
is_ti_method	definition
is_wrapper_with_dimred	add_dimred
is_wrapper_with_expression	add_expression
is_wrapper_with_feature_importance	add_feature_importance
is_wrapper_with_grouping	add_grouping
is_wrapper_with_milestone_labelling	label_milestones
is_wrapper_with_prior_information	add_prior_information
is_wrapper_with_timings	add_timings
is_wrapper_with_trajectory	add_trajectory
is_wrapper_with_waypoints	add_waypoints
is_wrapper_with_waypoint_cells	add_cell_waypoints
label_milestones	label_milestones
label_milestones_markers	label_milestones
priors	priors
prior_usages	prior_usages
project_milestones	project_trajectory
project_trajectory	project_trajectory
project_waypoints	project_waypoints
random_seed	random_seed
reexports	reexports
remove_root	add_root
select_waypoints	add_waypoints
select_waypoint_cells	add_cell_waypoints
set_default_config	reexports
simplify_igraph_network	simplify_igraph_network
simplify_trajectory	simplify_trajectory
test_docker_installation	reexports
test_h5_installation	reexports
test_singularity_installation	reexports
trajectory_types	trajectory_types
trajectory_type_dag	trajectory_type_dag
wrapper_types	wrapper_types
wrap_data	wrap_data
wrap_expression	wrap_expression
