Representing and Inferring Single-Cell Trajectories
Gather cells to their closest milestones
Generate the parameter documentation of a method, use with @eval
Get the default parameters of a method
Return all TI that are installed in one or more packages
Create a grouping from a trajectory
Infer one or more trajectories from a single-cell dataset
Label milestones either manually (label_milestones) or using marker ...
Add attraction of cells using RNA velocity
Construct a trajectory given its branch network and the pseudotime of ...
Constructs a trajectory using a graph between cells, by mapping cells ...
Add or select waypoint cells of a trajectory
Constructs a trajectory using a cell grouping and a network between gr...
Constructs a circular trajectory using the pseudotime values of each c...
Add or create a dimensionality reduction
Constructs a trajectory by projecting cells within a dimensionality re...
Constructs a multifurcating trajectory using end state probabilities
Add count and normalised expression values to a dataset
Add a feature importance to a dataset
Add a cell grouping to a dataset
Constructs a linear trajectory using pseudotime values
Add or compute prior information for a trajectory
Add or calculate pseudotime as distance from the root
Add a GRN to a dynwrap object
Root the trajectory
Add information on overall differentially expressed features
Add timings to a trajectory
Construct a trajectory given its milestone network and milestone perce...
Add or create waypoints to a trajectory
Calculate the attraction of cells to other cells using velocity
Calculate average values of a matrix
Calculate geodesic distances between cells in a trajectory
Layout the trajectory and its cells in 2 dimensions using a graph layo...
Classify a milestone network
Common param
Convert a definition loaded in from a yaml
Conversion between milestone percentages and progressions
Conversion between milestone percentages and progressions
Create a TI method from a docker / singularity container
Create a TI method from a local method definition file
Create a TI method from an R function wrapper
Meta information on an author
Meta information on the container in which the wrapper resides
Meta information on the manuscript
Define meta information on the TI method.
Meta information on the package in which the TI function resides
Meta information on the parameters of the TI method
Meta information on the wrapper
Create a definition
Method process definition
Inferring and adapting single-cell trajectories
Flip a set of edges of the milestone network
Project a trajectory onto a dimensionality reduction
Project waypoints of a trajectory (e.g. milestones) into a space defin...
Generate a random seed
Objects exported from other packages
Simplify an igraph network such that consecutive linear edges are remo...
Simplify a trajectory by removing transient milestones
A data wrapper for datasets and trajectories
Create a wrapper object with expression and counts
Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.