Representing and Inferring Single-Cell Trajectories

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) .

dynwrap: Representing and Inferring Single-Cell Trajectories

Tutorials Reference documentation

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 1.2.5

• BUG FIX convert_definition(): Fix for purrr having deprecated invoke in favour of exec (PR #166).

Recent changes in dynwrap 1.2.4

• Resubmission after babelwhale was removed from CRAN.

• MINOR CHANGE: Added @return documentation to all functions.

Dynverse dependencies