dynwrap: Representing and Inferring 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 1.2.5
- BUG FIX
convert_definition(): Fix for purrr having deprecated
invoke in favour of exec (PR #166).
Recent changes in dynwrap 1.2.4
Dynverse dependencies
