ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists

Raman Sethi, Kok Siong Ang, Mengwei Li, Yahui Long, Jingjing Ling and Jinmiao Chen ()
Additional contact information
Raman Sethi: Matrix
Kok Siong Ang: Proteos
Mengwei Li: Proteos
Yahui Long: Proteos
Jingjing Ling: Immunos
Jinmiao Chen: Matrix

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell’s streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application ( https://immunesinglecell.org/ezsc/ ) or a software package with a shinyApp interface ( https://github.com/JinmiaoChenLab/ezSingleCell2 ) for offline analysis.

Date: 2024
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DOI: 10.1038/s41467-024-48188-2

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