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.
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.
We welcome contributions from the scRNA-seq community! If you would like to contribute please follow the have a look at the 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.
If you are interested in joining the scRNA-tools team please contact us.
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
@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", bioRxiv (2021), DOI: 10.1101/2021.08.13.456196
@UNPUBLISHED{,
title = "Over 1000 tools reveal trends in the single-cell {RNA-seq}
analysis landscape",
author = "Zappia, Luke and Theis, Fabian J",
journal = "bioRxiv",
pages = "2021.08.13.456196",
month = aug,
year = 2021,
language = "en",
doi = "10.1101/2021.08.13.456196",
url = "https://doi.org/10.1101/2021.08.13.456196"
}