dynwrap

Representing and Inferring Single-Cell Trajectories


Keywords
trajectory-inference
License
GPL-3.0

Documentation

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 (unreleased)

Documentation

  • Added examples to all functions

New features

  • 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

Dynverse dependencies