Interactive analysis of single-cell data using flexible workflows with SCTK2

• DOI: 10.1016/j.patter.2023.100814
• Publication Date: 2023-08-03T14:40:45Z
• Authors: Yichen Wang; Irzam Sarfraz; Nida Pervaiz; Rui Hong; Yusuke Koga; Vidya Akavoor; Xinyun Cao; Salam Alabdullatif; Syed Ali Zaib; Zhe Wang; Frederick Jansen; Masanao Yajima; W. Evan Johnson; Joshua D. Campbell
• Keywords: Graphical user interface; Interface (matter); Data type

Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity complex biological systems. Many tools and workflows have been developed to perform different types analyses. However, these are spread across packages or programming environments, rely on underlying structures, only be utilized by people with knowledge languages. In Single-Cell Toolkit 2 (SCTK2), we integrated a variety popular various aspects scRNA-seq analysis. All run in R console using an intuitive graphical user interface built R/Shiny. HTML reports generated Rmarkdown used document recapitulate individual steps entire analysis workflows. We show that toolkit offers more features when compared existing allows for seamless non-computational users.