webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration.


Integrative analysis of single-cell RNA-sequencing (scRNA-seq) data with spatial data for the same species and organ would provide each cell sample with a predictive spatial location, which would facilitate biological study. However, publicly available spatial sequencing datasets for specific species and organs are rare and are often displayed in different formats. In this study, we introduce a new web-based scRNA-seq analysis tool, webSCST, that integrates well-organized spatial transcriptome sequencing datasets categorized by species and organs, provides a user-friendly interface for raw single-cell processing with popular integration methods and allows users to submit their raw scRNA-seq data once to obtain predicted spatial locations for each cell type. webSCST implemented in shiny with all major browsers supported is available at http://www.webscst.com. webSCST is also freely available as an R package at https://github.com/swsoyee/webSCST.


Spatial Transcriptomics

MeSH terms

Sequence Analysis, RNA
Single-Cell Analysis
Gene Expression Profiling


Zhang, Zilong
Cui, Feifei
Su, Wei
Dou, Lijun
Xu, Anqi
Cao, Chen
Zou, Quan

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