README.Rmd

---
output:
  github_document:
    html_preview: false
editor_options: 
  chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.path = "man/figures/README_", warning=FALSE, message=FALSE, error=FALSE, echo = TRUE)

library(tidyverse)
submission_to_cran <- FALSE
```

# dyngen <img src="man/figures/logo.png" align="right" />

<!-- badges: start -->

[![CRAN Status](https://www.r-pkg.org/badges/version/dyngen)](https://cran.r-project.org/package=dyngen)
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/dyngen)](https://cran.r-project.org/package=dyngen)
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dyngen is a novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods.

dyngen is now published (CC-BY, [doi:10.1038/s41467-021-24152-2](https://doi.org/10.1038/s41467-021-24152-2)). Run `citation("dyngen")` to obtain the corresponding citation information. All source code for reproducing the results in this manuscript are available on [GitHub](https://github.com/dynverse/dyngen_manuscript).

```{r out.width = '60%', echo = FALSE}
knitr::include_graphics("man/figures/overview.png")
```

## Installation
dyngen should work straight out of the CRAN box by running `install.packages("dyngen")`. Having said that, you should definitely configure a few system variables for optimal speed. Check the [installation guide](https://dyngen.dynverse.org/articles/installation.html) for more information!

## Getting started

Check out [this guide](https://dyngen.dynverse.org/articles/getting_started.html) on how to get started with dyngen. You can find more guides by clicking any of the links below:

```{r vignettes, results='asis', echo=FALSE}
vign <- list.files("vignettes", pattern = "*.Rmd", recursive = TRUE)
walk(
  c(vign[!grepl("^advan", vign)], vign[grepl("^advan", vign)]),
  function(file) {
    title <- 
      read_lines(paste0("vignettes/", file)) %>% 
      keep(~grepl("^title: ", .)) %>% 
      gsub("title: \"(.*)\"", "\\1", .)
    vignette_name <- gsub("\\.Rmd", "", file)
    html_name <- gsub("\\.Rmd", ".html", file)
    
    cat("* [", title, "](https://dyngen.dynverse.org/articles/", html_name, ")\n", sep = "")
  }
)
```

## Latest changes

A full list of changes is available on our [changelog](https://dyngen.dynverse.org/news/index.html).