dockerpjhuang/shinysc repository overview

ShinySC is a user-friendly, R/Shiny-based desktop application for comprehensive single-cell RNA-seq analysis, tailored for researchers without programming skills. It supports diverse input formats (10x Genomics, Seurat, Scanpy, BD Rhapsody, CellView) and integrates key functions including quality control, normalization, clustering, batch correction, differential expression, trajectory inference, and multiple cell-type annotation methods (SingleR, ScType, scCATCH, GPTCelltype). Benchmarking shows reliable performance on datasets with up to 200,000 cells using standard desktops (64 GB RAM). Demonstrations on PBMC datasets validate its accuracy and usability. ShinySC is freely available for Windows, macOS, and Linux: http://tardis.cgu.edu.tw/ShinySC⁠.

If you find ShinySC beneficial to your research, please cite the following reference:

ShinySC: an R/Shiny-based desktop application for seamless analysis of scRNA-Seq data. Biomedical Journal. 2025 Jul 1:100885. doi: 10.1016/j.bj.2025.100885.