scX: a user-friendly tool for scRNAseq exploration

• DOI: 10.1093/bioadv/vbae062
• Publication Date: 2024-05-02T20:37:13Z
• Authors: Tomás V Waichman; M L Vercesi; Ariel A Berardino; Maximiliano S Beckel; Damiana Giacomini; Natalí B Rasetto; Magalí Herrero; Daniela J Di Bella; Paola Arlotta; Alejandro F Schinder; Ariel Chernomoretz
• Keywords: User Friendly

Abstract Motivation Single-cell RNA sequencing (scRNAseq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. Results In this article, we present scX, an R package built on Shiny framework that streamlines analysis, exploration, visualization of single-cell experiments. With interactive graphic interface, implemented as a web application, scX provides easy access key scRNAseq analyses, including marker identification, gene expression profiling, differential analysis. Additionally, seamlessly integrates with commonly used Seurat SingleCellExperiment objects, resulting in efficient processing varied datasets. Overall, serves valuable user-friendly tool effortless exploration sharing data, simplifying some complexities inherent Availability implementation Source code can be downloaded from https://github.com/chernolabs/scX. A docker image available dockerhub chernolabs/scx.