Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published March 28, 2022 | Supplemental Material + Published
Journal Article Open

WormBase single-cell tools


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.

Attached Files

Published - vbac018.pdf

Supplemental Material - vbac018_supplementary_data.pdf


Files (3.0 MB)
Name Size Download all
2.3 MB Preview Download
635.6 kB Preview Download

Additional details

August 22, 2023
December 22, 2023