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
news(package = "dynwrap") or NEWS.md for a full
list of changes.
Recent changes in dynwrap 1.2 (unreleased)
- Added examples to all functions
- Improved RNA velocity handling:
- Not all features need to be present in the projected expression, allowing integration with standard velocyto.R pipelines
Recent changes in dynwrap 1.1.4 (27-06-2019)
- BUG FIX: Fixed #142 where the error message was truncated