README.Rmd

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

```{r, echo = FALSE, message = FALSE, error = FALSE, warning = FALSE}
library(tidyverse)
library(dynmethods)

data("methods")
methods <- methods %>% filter(!method_source %in% c("control")) # controls are not actual TI methods
```

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[**ℹ️ Tutorials**](https://dynverse.org) &nbsp; &nbsp;
[**ℹ️ Reference documentation**](https://dynverse.org/reference/dynmethods)
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<br><img src="man/figures/logo.png" align="right" />
# A collection of `r nrow(methods)` trajectory inference methods
This package contains wrappers for trajectory inference (TI) methods. The output of each method is transformed into a common trajectory model using [dynwrap](https://www.github.com/dynverse/dynwrap), which allows easy [visualisation and comparison](https://www.github.com/dynverse/dyno). All methods are wrapped inside a docker container, which avoids dependency issues, and also makes it easy to add a new method.

**To run any of these methods, interpret the results and visualise the trajectory, see the [dyno package](https://www.github.com/dynverse/dyno).**

To include your own method, feel free to send us a [pull request](https://github.com/dynverse/dynmethods/pulls) or create an [issue](https://github.com/dynverse/dynmethods/labels/new%20method). The easiest way to add a new method is [through a docker container](https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html), so that dependencies don't pose any issues for other users, but we also welcome methods [directly wrapped inside of R](https://dynverse.github.io/dynwrap/articles/create_ti_method_r.html). The main benefit of adding your own method is that users can easily compare your method with others and [visualise/interpret the output](https://www.github.com/dynverse/dyno). Moreover, your method will be compared to other methods within [the TI method evaluation](https://doi.org/10.1101/276907).


## List of included methods

```{r, echo = FALSE, warning = FALSE, error = FALSE, message = FALSE, results='asis'}
df <-
  methods %>% 
  arrange(method_name) %>% 
  mutate(
    docker_url = paste0("https://hub.docker.com/r/", container_docker),
    docker_svg = paste0("https://img.shields.io/docker/v/", container_docker, "/latest?logo=docker"),
    github_actions_svg = paste0("https://github.com/", container_docker, "/workflows/make/badge.svg"),
    github_actions_link = paste0("https://github.com/", container_docker, "/actions?query=workflow%3Amake"),
    Method = method_name,
    Doi = map_chr(manuscript_doi, function(do) if (!is.null(do) && !is.na(do)) paste0("<a href='https://doi.org/", do, "'><img src='man/figures/doi_logo.png' height='16'></a>") else "" ),
    Docker = paste0("[![Version](", docker_svg, ")](", docker_url, ")"),
    Code = paste0("[code](", container_url, ")"), 
    Status = paste0("[![Build status](", github_actions_svg, ")](", github_actions_link, ")"), 
    Authors = map_chr(method_authors, function(authors) {
      if (length(authors) > 0) {
          
        first <- authors[[1]]
        if (length(first) == 1 && is.na(first)) {
          return("")
        }
        map_chr(authors, function(author) {
          if (is.null(author$family)) {
            author$family <- ""
          }
          author_text <- paste0(author$given, " ", author$family)
  
          if (!is.null(author$ORCID)) {
            author_text <- paste0(author_text, " <a href='https://orcid.org/", author$ORCID, "'><img src='man/figures/orcid_logo.svg' height='16'></a>")
          }
  
          if (!is.null(author$github)) {
            author_text <- paste0(author_text, " <a href='https://github.com/", author$github, "'><img src='man/figures/github_logo.png' height='16'></a>")
          }
  
          author_text %>% paste0("<sub>", ., "</sub>")
        }) %>% paste0(collapse = "<br>")
      } else {
        ""
      }
    })
  )

df %>% 
  select(Method, Doi, Code, Docker, Status, Authors) %>% 
  knitr::kable()
```

## Sources

We used following resources to get a (hopefully exhaustive) list of all TI methods:

[Anthony Gitter's single-cell-pseudotime](https://github.com/agitter/single-cell-pseudotime) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1297423.svg)](https://doi.org/10.5281/zenodo.1297423)

[Sean Davis' awesome-single-cell](https://github.com/seandavi/awesome-single-cell)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1294021.svg)](https://doi.org/10.5281/zenodo.1294021)

[Luke Zappia's scRNA-tools](https://www.scrna-tools.org)
[![DOI](https://zenodo.org/badge/DOI/10.1101/206573.svg)](https://doi.org/10.1101/206573)

## New methods

Some methods are not wrapped (yet). Check out the [issues](https://github.com/dynverse/dynmethods/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3Anew_method) for an overview

## Latest changes

Check out `news(package = "dynwrap")` or [NEWS.md](NEWS.md) for a full list of changes.

<!-- This section gets automatically generated from 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)