WormBase single-cell tools
Eduardo da Veiga Beltrame, Valerio Arnaboldi, Paul W. Sternberg
Abstract
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.
Topics & Concepts
Computer scienceSource codeVisualizationCode (set theory)Caenorhabditis elegansWorld Wide WebComputational biologyData miningBiologyGeneProgramming languageGeneticsSet (abstract data type)Single-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model OrganismsGene Regulatory Network Analysis