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Single cell tools for WormBase

da Veiga Beltrame, Eduardo and Arnaboldi, Valerio and Sternberg, Paul W. (2021) Single cell tools for WormBase. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210712-143510822

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Abstract

We present two web apps for interactively performing common tasks with single cell RNA sequencing data: scdefg for interactive differential expression and wormcells-viz for visualization of gene expression. We made these tools available with public C. elegans datasets curated by WormBase at single-cell.wormbase.org. They can also be readily deployed for use with any other datasets using the source code available at github.com/WormBase/scdefg and at github.com/WormBase/wormcells-viz.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.07.04.451030DOIDiscussion Paper
https://single-cell.wormbase.org/Related ItemData/Code
https://github.com/WormBase/scdefgRelated ItemData/Code
https://github.com/WormBase/wormcells-vizRelated ItemData/Code
https://github.com/WormBase/anndata-wranglingRelated ItemData/Code
ORCID:
AuthorORCID
da Veiga Beltrame, Eduardo0000-0002-1529-9207
Arnaboldi, Valerio0000-0002-2563-5374
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors. This version posted July 4, 2021. The authors would like to thank Paulo Nuin for reviewing the code, Tom Morrell for assistance with CaltechData, and Valentine Svensson for suggestions on the manuscript. This work was supported by grants NIH U24HG010859 and NIH U24HG002223.
Group:WormBase
Funders:
Funding AgencyGrant Number
NIHU24HG010859
NIHU24HG002223
Record Number:CaltechAUTHORS:20210712-143510822
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210712-143510822
Official Citation:Single cell tools for WormBase. Eduardo da Veiga Beltrame, Valerio Arnaboldi, Paul W. Sternberg. bioRxiv 2021.07.04.451030; doi: https://doi.org/10.1101/2021.07.04.451030
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109773
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:12 Jul 2021 15:00
Last Modified:12 Jul 2021 15:00

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