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README.Rmd
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---
title: "dynwrap: Representing and Inferring Single-Cell Trajectories"
output:
github_document:
html_preview: false
editor_options:
chunk_output_type: console
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE, message = FALSE, error = FALSE, warning = FALSE}
library(tidyverse)
```
<!-- badges: start -->
[](https://github.com/dynverse/dynwrap/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/dynverse/dynwrap?branch=master)
[**Tutorials**](https://dynverse.org)
[**Reference documentation**](https://dynverse.org/reference/dynwrap/)
<!-- badges: end -->
<img src="man/figures/logo.png" align="right" />
**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](https://github.com/dynverse/dynmethods).
The advantage of using a common model is that it allows:
* Comparison between a prediction and a gold standard, eg. using [dyneval](https://github.com/dynverse/dyneval)
* Comparing two predictions
* Easily visualise the trajectory, eg. using [dynplot](https://github.com/dynverse/dynplot)
* Extracting relevant features/genes, eg. using [dynfeature](https://github.com/dynverse/dynfeature)
## Latest changes
Check out `news(package = "dynwrap")` or [NEWS.md](NEWS.md) for a full list of changes.
<!-- This section gets automatically generated from inst/NEWS.md -->
```{r news, echo=FALSE, results="asis"}
cat(dynutils::recent_news())
```
## Dynverse dependencies
<!-- Generated by "update_dependency_graphs.R" in the main dynverse repo -->
