README.Rmd

---
output: 
  github_document:
    toc: TRUE
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

[![Build Status](https://travis-ci.org/dynverse/dynplot.svg?branch=master)](https://travis-ci.org/dynverse/dynplot) 
[![codecov](https://codecov.io/gh/dynverse/dyno/branch/master/graph/badge.svg)](https://codecov.io/gh/dynverse/dyno) 
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/dynverse/dyno?branch=master&svg=true)](https://ci.appveyor.com/project/dynverse/dyno) 
[**ℹ️ Tutorials**](https://dynverse.org)  &nbsp;  &nbsp; 
[**ℹ️ Reference documentation**](https://dynverse.org/reference) <br><img src="man/figures/dyno.gif" align="right" width="150px" />

# Inferring trajectories using dyno

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%",
  fig.path = "man/figures/",
  message = FALSE,
  dpi = 300
)
set.seed(1)
```

The **dyno** package offers **end-users** a complete TI pipeline. It features:

* a uniform interface to `r nrow(dynmethods::methods)` [TI methods](https://github.com/dynverse/dynmethods#list-of-included-methods),
* an [interactive guideline tool](https://github.com/dynverse/dynguidelines#selecting-the-most-optimal-ti-methods) to help the user select the most appropriate method,
* [streamlined interpretation and visualisation of trajectories](https://dynverse.org/reference/dynplot/plot_trajectory/plot_dimred/#examples), including colouring by gene expression or clusters, and
* downstream analyses such as the [identification of potential marker genes](https://dynverse.org/reference/dynplot/plot_trajectory/plot_heatmap/#examples).

**For information on how to use dyno, check out the installation instructions, tutorials and documentation at [dynverse.org](https://dynverse.org)**

![](man/figures/toolkit.png)

## Latest changes

Check out `news(package = "dyno")` 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 -->
![](man/figures/dependencies.png)