.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_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_root_using_expression |
Root the trajectory |
add_tde_overall |
Add information on overall differentially expressed features |
add_timings |
Add timings to a trajectory |
add_timing_checkpoint |
Add timings to a trajectory |
add_trajectory |
Construct a trajectory given its milestone network and milestone percentages or progressions |
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 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 |
compute_tented_geodesic_distances |
Calculate geodesic distances between cells in a trajectory |
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 |
definition |
Create a definition |
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 |
determine_cell_trajectory_positions |
Add or select waypoint cells of a trajectory |
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 @eval |
generate_prior_information |
Add or compute prior information for a trajectory |
get_default_parameters |
Get the default parameters of a method |
get_dimred |
Add or create a dimensionality reduction |
get_expression |
Add count and normalised expression values to a dataset |
get_grouping |
Add a cell grouping to a dataset |
get_milestone_labelling |
Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers') |
get_ti_methods |
Return all TI that are installed in one or more packages |
group_from_trajectory |
Create a grouping from a trajectory |
group_onto_nearest_milestones |
Create a grouping from a trajectory |
group_onto_trajectory_edges |
Create a grouping from a trajectory |
infer_trajectories |
Infer one or more trajectories from a single-cell dataset |
infer_trajectory |
Infer one or more trajectories from a single-cell dataset |
is_data_wrapper |
A data wrapper for datasets and trajectories |
is_rooted |
Root the trajectory |
is_ti_method |
Create a definition |
is_wrapper_with_dimred |
Add or create a dimensionality reduction |
is_wrapper_with_expression |
Add count and normalised expression values to a dataset |
is_wrapper_with_feature_importance |
Add a feature importance to a dataset |
is_wrapper_with_grouping |
Add a cell grouping to a dataset |
is_wrapper_with_milestone_labelling |
Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers') |
is_wrapper_with_prior_information |
Add or compute prior information for a trajectory |
is_wrapper_with_timings |
Add timings to a trajectory |
is_wrapper_with_trajectory |
Construct a trajectory given its milestone network and milestone percentages or progressions |
is_wrapper_with_waypoints |
Add or create waypoints to a trajectory |
is_wrapper_with_waypoint_cells |
Add or select waypoint cells of a trajectory |
label_milestones |
Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers') |
label_milestones_markers |
Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers') |
priors |
Metadata on priors |
prior_usages |
Metadata on prior usages |
project_milestones |
Project a trajectory onto a dimensionality reduction |
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 |
remove_root |
Root the trajectory |
select_waypoints |
Add or create waypoints to a trajectory |
select_waypoint_cells |
Add or select waypoint cells of 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_types |
Metadata on the trajectory types |
trajectory_type_dag |
A DAG connecting different trajectory types |
wrapper_types |
Metadata on wrapper types |
wrap_data |
A data wrapper for datasets and trajectories |
wrap_expression |
Create a wrapper object with expression and counts |