![scRNA-tools](docs/img/banner.png)

# scRNA-tools

[![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![Build Status](https://github.com/scRNA-tools/scRNA-tools/actions/workflows/build_site.yml/badge.svg)](https://github.com/scRNA-tools/scRNA-tools/actions/workflows/build_site.yml)
[![Netlify Status](https://api.netlify.com/api/v1/badges/e1fce3cd-d1e6-439d-8751-83360c631b5d/deploy-status)](https://app.netlify.com/sites/scrna-tools/deploys)

A database of software tools for the analysis of single-cell RNA-seq data. To
make it into the database software must be available for download and public use
somewhere (CRAN, Bioconductor, PyPI, Conda, GitHub, Bitbucket, a private website
etc). To view the database head to https://www.scRNA-tools.org.

## Purpose

This database is designed to be an overview of the currently available scRNA-seq
analysis software, it is unlikely to be 100% complete or accurate but will be
updated as new software becomes available.

## Contributing

We welcome contributions from the scRNA-seq community! If you would like to
contribute please follow the have a look at
[the wiki](https://github.com/scRNA-tools/scRNA-tools/wiki) or fill in the submission
form on our website (https://www.scrna-tools.org/submit). Please be aware that
by contributing you are agreeing to abide by the [code of conduct](CODE_OF_CONDUCT.md).

If you are interested in joining the scRNA-tools team please
[contact us](https://www.scRNA-tools.org/contact.html).

## Citation

If you find the scRNA-tools database useful for your work please cite our
publication:

> Zappia L, Phipson B, Oshlack A. _"Exploring the single-cell RNA-seq
> analysis landscape with the scRNA-tools database"_, **PLOS Computational
> Biology** (2018), DOI: [10.1371/journal.pcbi.1006245](https://doi.org/10.1371/journal.pcbi.1006245)

```bibtex
@ARTICLE{,
  title       = "Exploring the single-cell {RNA-seq} analysis landscape with
                 the {scRNA-tools} database",
  author      = "Zappia, Luke and Phipson, Belinda and Oshlack, Alicia",
  journal     = "PLoS Computational Biology",
  volume      =  14,
  number      =  6,
  pages       = "e1006245",
  month       =  jun,
  year        =  2018,
  language    = "en",
  doi         = "10.1371/journal.pcbi.1006245",
  url         = "https://doi.org/10.1371/journal.pcbi.1006245",
}
```

If you make use of our analysis of the first 1000 tools in the database please
also cite:

> Zappia L, Theis FJ. _"Over 1000 tools reveal trends in the single-cell RNA-seq
> analysis landscape"_, **Genome Biology** (2021),
> DOI: [10.1186/s13059-021-02519-4](https://doi.org/10.1186/s13059-021-02519-4)

```bibtex
@ARTICLE{,
  title    = "Over 1000 tools reveal trends in the single-cell {RNA-seq}
              analysis landscape",
  author   = "Zappia, Luke and Theis, Fabian J",
  journal  = "Genome Biol.",
  volume   =  22,
  number   =  1,
  pages    = "301",
  month    =  oct,
  year     =  2021,
  language = "en"
  doi      = "10.1186/s13059-021-02519-4",
  url      = "https://doi.org/10.1186/s13059-021-02519-4"
}
```