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Tools for inferring and wrapping single-cell trajectories

dynwrap contains the code for a common model of single-cell trajectories. The package can:

Wrap the input data of a trajectory inference method, such as expression and prior information
Run a trajectory inference method in R, in a docker container or a singularity container
Wrap the output of a trajectory inference method, such as the pseudotime, a clustering or a branch network, and convert it into a common trajectory model
Further postprocess and adapt the trajectory model, such as labelling the milestones and rooting the trajectory

Documentation and the API reference for dynwrap can be found at the dyvnerse documentation website: https://dynverse.org/ .

dynwrap was used to wrap 50+ trajectory inference method within docker containers in dynmethods.

The advantage of using a common model is that it allows:

Latest changes

Check out news(package = "dynwrap") or NEWS.md for a full list of changes.

BUG FIX project_trajectory(): Correctly pass parameters.
MINOR CHANGES select_waypoints(): Do not recompute waypoints if trajectory already contains some.
MINOR CHANGES convert_progressions_to_milestone_percentages(): Solve tapply issues ahead of dplyr 1.0 release.

FUNCTIONALITY: Improved RNA velocity handling. Not all features need to be present in the projected expression, allowing integration with standard velocyto.R pipelines.
BUG FIX calculate_pseudotime(): Fix pseudotime calculation on branching trajectories (#139).
BUG FIX flip_edges(): Also flip dimred_segment_progressions if available.
BUG FIX add_root(): Fix rooting for some linear trajectories (#149)
MINOR CHANGES: Allow a named vector for groups_id prior information (#154)
MINOR CHANGES: Moved orient_topology_to_velocity() to scvelo R package.
BUG FIX simplify_trajectory(): handle dimred_milestones and dimred_segments values (#153).
BUG FIX add_dimred(): Do not execute example of dyndimred if is not installed.