WormBase single-cell tools

Creators: da Veiga Beltrame, Eduardo; Arnaboldi, Valerio; Sternberg, Paul W.

Abstract

We present two web apps for interactively performing common tasks with single-cell RNA sequencing data: scdefg for differential expression and wormcells-viz for visualization of gene expression. We deployed these tools with public Caenorhabditis elegans datasets curated by WormBase at https://single-cell.wormbase.org. Source code for deploying these tools with other datasets is available at https://github.com/WormBase/scdefg and https://github.com/WormBase/wormcells-viz.

Additional Information

© The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 07 September 2021. Revision received: 28 February 2022. Editorial decision: 19 March 2022. Accepted: 26 March 2022. Published: 28 March 2022. Corrected and typeset: 06 July 2022. The authors would like to thank Paulo Nuin and David Brown for reviewing the code, Tom Morrell for assistance with CaltechData and Valentine Svensson for suggestions on the manuscript. Author contributions. E.B. conceived the tools design and curated the data. E.B. implemented scefg with input from V.A. V.A. implemented wormcells-viz with input from E.B. E.B., V.A. and P.W.S. wrote and reviewed the manuscript. This work was supported by grant numbers NIH U24HG010859 and NIH U24HG002223. Conflict of Interest: none declared.

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