Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Abstract

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records of the growth of the field over time.\n\nAuthor summaryIn recent years single-cell RNA-sequeing technologies have emerged that allow scientists to measure the activity of genes in thousands of individual cells simultaneously. This means we can start to look at what each cell in a sample is doing instead of considering an average across all cells in a sample, as was the case with older technologies. However, while access to this kind of data presents a wealth of opportunities it comes with a new set of challenges. Researchers across the world have developed new methods and software tools to make the most of these datasets but the field is moving at such a rapid pace it is difficult to keep up with what is currently available. To make this easier we have developed the scRNA-tools database and website (www.scRNA-tools.org). Our database catalogues analysis tools, recording the tasks they can be used for, where they can be downloaded from and the publications that describe how they work. By looking at this database we can see that developers have focued on methods specific to single-cell data and that they embrace an open-source approach with permissive licensing, sharing of code and preprint publications.