ℹ️ Tutorials ℹ️ Reference documentation
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:
- Comparison between a prediction and a gold standard, eg. using dyneval
- Comparing two predictions
- Easily visualise the trajectory, eg. using dynplot
- Extracting relevant features/genes, eg. using dynfeature
Latest changes
Check out news(package = "dynwrap")
or NEWS.md for a full
list of changes.
Recent changes in dynwrap 1.2.1 (2020-05-11)
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.
Recent changes in dynwrap 1.2.0 (2020-03-09)
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 flipdimred_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.