FAQs

Frequently asked questions about scRNA-tools

What is scRNA-tools?: scRNA-tools is a catalogue of software packages designed for the analysis of single-cell RNA-sequencing data. We aim to record details of all tools for working with this data type.
Where is my tool?: If you have a tool that we are missing please fill in our submission form or submit an issue to our GitHub repository. We would love to add it!
That's not right, can you fix it?: We try to keep everything up to date but it's a difficult task. If you notice that the details for a tool are incorrect or need updating please fill in our submission form or submit an issue to our GitHub repository.
I'm on Safari, why do things look funny?: The site has been developed using Chrome. While we try to accommodate other browsers this can be difficult and there are some known issues with Safari. If you run into problems try loading scRNA-tools.org in Chrome.
Who are we?: scRNA-tools.org was created by the Oshlack lab, a bioinformatics lab based in Melbourne, Australia.

The resource is now maintained by a team of volunteers around the world including at the Institute of Computational Biology in Munich, Germany.
How can I get involved?: We encourage and welcome contributions from the community via our submission form and GitHub repository.

We are always look for volunteers to join the scRNA-tools team. If you are interested in becoming involved in a more formal way please contact us.
What is low-maintenance mode?: From May 2024 scRNA-tools will be entering low-maintenance mode. This means that we will no longer be actively actively seeking out new tools to add to the database. However, the database will still be maintained and updated based on user submissions. If you have a tool that you would like to add or update please fill in our submission form and we will add it as soon as we can. You can read more about this decision in this blog post.
How can I cite scRNA-tools.org?: If you find the scRNA-tools database useful for your work please cite our paper:

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

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