{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/scx-a-user-friendly-tool-for-scrna-seq","title":"scX: A user-friendly tool for scRNA-seq exploration","arxiv_id":"2311.00012","date":"2023-10-31","proceeding":null,"authors":["Tomás Vega Waichman","M. Luz 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"],"abstract":"Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on the Shiny framework that streamlines the analysis, exploration, and visualization of single-cell experiments. With an interactive graphic interface, implemented as a web application, scX provides easy access to key scRNAseq analyses, including marker identification, gene expression profiling, and differential gene expression analysis. Additionally, scX seamlessly integrates with commonly used single-cell Seurat and SingleCellExperiment R objects, resulting in efficient processing and visualization of varied datasets. Overall, scX serves as a valuable and user-friendly tool for effortless exploration and sharing of single-cell data, simplifying some of the complexities inherent in scRNAseq analysis.","url_abs":"https://arxiv.org/abs/2311.00012v2","url_pdf":"https://arxiv.org/pdf/2311.00012v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"scx-a-user-friendly-tool-for-scrna-seq","repo_url":"https://github.com/chernolabs/scx","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}