Background

Single-cell RNA sequencing (scRNA-seq) enables the profiling of tens to hundreds of thousands of cells in a single experiment, offering unprecedented resolution for studying gene expression. This technique significantly enhances the ability to identify novel cell types, states, and dynamics in complex biological systems across a wide variety of tissues and organisms. Despite extensive efforts by computational biologists to streamline single-cell data analysis through various software packages, novices and non-computational users still face challenges due to diverse data formats, cumbersome analysis steps, and scattered algorithms across different programming languages.

What we have done?

Multi-Format Support

To address the aforementioned barriers, we present ShinySC, an R/Shiny-based desktop application designed for seamless scRNA-seq data analysis, accessible to users without programming experience. ShinySC features an easy-to-use GUI and supports various input formats, including 10X Genomics Cell Ranger (MEX and HDF5), Seurat Object (.rds), Scanpy (.h5ad), BD Rhapsody (.csv), and CellView(.Rds).

Key Functions

ShinySC offers a comprehensive suite of functions, including Quality Control, Normalization, Feature Selection, Dimensionality Reduction, Clustering, Marker Gene Identification, Batch Effect Correction and Differential Expression Analysis across Experimental Conditions, as well as Trajectory Inference. These functionalities are built on the Seurat and visual analytics packages, supplemented by our in-house scripts, offering enhanced visualization, dynamic parameter adjustments, and downloadable publication-ready figures.

Automatic Cell-type Annotation

ShinySC integrates marker-based annotation approaches (ScType and scCATCH), reference-based annotation method (SingleR)and the latest GPT-4 annotation (GPTCelltype) strategy to automatically annotate cell types, making scRNA-seq analysis more accessible to researchers with limited computational expertise. As far as we know, ShinySC is the first desktop application of its kind that provides a one-stop solution for single-cell analysis.

Annotation Refinement

A unique feature of ShinySC is its annotation refinement capability, allowing users to review and refine initial annotations using an integrated summary table that compares results across different annotation methods.

Cross-platform Support

ShinySC leverages R Shiny, shiny dashboard, DesktopDeployR, and Docker Desktop to create a robust desktop application for both Windows and Mac platforms, ensuring network independence and data security.

The Framework of ShinySC

Documentation

Welcome to ShinySC’s documentation

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