dweemx / dynwrap

A common data format and inference environment for single-cell trajectories 📦

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 the trajectory model, such as labelling the milestones and rooting the trajectory

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.

Latest changes in dynwrap 0.3.1.1 (17-12-2018)

• CLEAN UP: Removed helper functions that are not required any more: get_env_or_null(), read_rds_or_null() and print_processx().

• MINOR CHANGE: remove requirement that milestone_ids and cell_ids cannot overlap

Latest changes in dynwrap 0.3.1 (19-11-2018)

• HOTFIX: Use utils::data() to get access to priors.