scExplorer: a comprehensive web server for single-cell RNA sequencing data analysis

TL;DR

scExplorer is a web-based platform that makes single-cell RNA sequencing data analysis accessible and reproducible for researchers without programming skills.

Contribution

The novel contribution is a web server with integrated batch correction, scalable job scheduling, and reproducible reporting for scRNA-seq analysis.

Findings

scExplorer supports comprehensive batch correction using four advanced algorithms.

The platform enables scalable job management with SLURM-based scheduling and pause/resume functionality.

Automated report generation ensures reproducibility and transparency in scRNA-seq analysis.

Abstract

Computational analysis of single-cell RNA sequencing (scRNA-seq) data presents significant barriers for researchers lacking programming expertise, particularly for multi-dataset integration, scalable job management, and reproducible workflows. We developed scExplorer, a web-based platform that addresses these limitations through three key innovations: Comprehensive batch correction using four state-of-the-art algorithms (ComBat, Scanorama, BBKNN, and Harmony), SLURM-based job scheduling with pause/resume functionality for large-scale analyses, and automated generation of publication-ready reports with exportable configuration files ensuring complete reproducibility. The platform’s modular Docker architecture supports both standalone and client–server deployments, enabling analysis of datasets ranging from thousands to hundreds of thousands of cells. An openly documented REST API clarifies how the interface orchestrates analyses and supports transparent operation. scExplorer eliminates the technical barriers that prevent non-computational researchers from performing rigorous scRNA-seq analysis while maintaining the transparency and reproducibility standards required for collaborative research.

https://apps.cienciavida.org/scexplorer/.

Figures