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. 2022 Mar 28;2(1):vbac018.
doi: 10.1093/bioadv/vbac018. eCollection 2022.

WormBase single-cell tools

Eduardo da Veiga Beltrame  1 , Valerio Arnaboldi  1 , Paul W Sternberg  1
Affiliations

WormBase single-cell tools

Eduardo da Veiga Beltrame et al. Bioinform Adv. .

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.

Supplementary information: Supplementary data are available at Bioinformatics Advances online.

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Figures

Fig. 1.
Fig. 1.
Overview of the process to go from gene count matrix to deployment of the apps. Training an scVI model can be done quickly and only requires starting from the gene count matrices as outputted by standard alignment software such as Cell Ranger (Zheng et al., 2017). The scdefg app only requires as input the trained scVI model as saved by scvi-tools, while wormcells-viz requires using our pipeline to create the custom input anndatas. See Supplementary Material for detailed explanation
See this image and copyright information in PMC

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