Year: 2024
Type: article
Abstract: Summary: 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. Availability and implementation: https://apps.cienciavida.org/scexplorer/.
Source: Bioinformatics Advances
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,917
Awards: COLLECTIVE MIND: FROM COMPUTATIONAL MODELING TO COMPUTATIONAL SOCIOLOGY. UNVEILING THE ROLE OF SELF AND SITUATIONAL AWARENESS IN AGENT-BASED SYSTEMS (ABSS)., LABORATORIO NACIONAL DE SUPERCOMPUTACION, UNVEILING THE HELPER ROLE OF TREG CELLS IN LONG-LASTING CD8 T CELL IMMUNITY INDUCED BY CANCER IMMUNOTHERAPY, CARACTERIZACION DE LAS SUBPOBLACIONES DE LINFOCITOS T CD8+ DE MEMORIA RESIDENTE DE TUMOR PRIMARIO Y NODULOS LINFATICOS INVADIDOS DE CANCER DE MAMA, CENTRO CIENTIFICO TECNOLOGICO DE EXCELENCIA CIENCIA & VIDA (CIENCIA & VIDA)
OpenAlex ID: W4415830222