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ℹ️ Tutorials    ℹ️ Referencedocumentation

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

• Wrap the input data of a trajectory inference method, such asexpression and prior information
• Run a trajectory inference method in R, in a docker container or asingularity container
• Wrap the output of a trajectory inference method, such as thepseudotime, a clustering or a branch network, and convert it into acommon trajectory model
• Further postprocess and adapt the trajectory model, such aslabelling the milestones and rooting the trajectory

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

dynwrap was used to wrap 50+ trajectory inference method within dockercontainers indynmethods.

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

• Comparison between a prediction and a gold standard, eg. usingdyneval
• Comparing two predictions
• Easily visualise the trajectory, eg. usingdynplot
• Extracting relevant features/genes, eg. usingdynfeature

Check outnews(package = "dynwrap") orNEWS.md for a fulllist of changes.

• MAJOR CHANGEconvert_milestone_percentages_to_progressions():Rewrite implementation to attain significant speedup.

• MINOR CHANGEinfer_trajectory(): Infer command (Rscript/python)from file extension if possible and avoid using shebang to executescript, because R CMD check for R 4.0 puts Rscript and R dummyexecutables on the path before R CMD check. This means#!/usr/bin/env Rscript does not work anymore.

• BUG FIXproject_waypoints(): Rename milestone waypoints such thatthe names are unique.

• BUG FIXinfer_trajectory(): Fix error message printing.

• BUG FIXproject_trajectory(): Correctly pass parameters.

• MINOR CHANGESselect_waypoints(): Do not recompute waypoints iftrajectory already contains some.

• MINOR CHANGESconvert_progressions_to_milestone_percentages():Solve tapply issues ahead of dplyr 1.0 release.