Abstract
SUMMARY: Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression at the individual cell level, unraveling unprecedented insights into cellular heterogeneity. However, the analysis of scRNA-seq data remains a challenging and time-consuming task, often demanding advanced computational expertise, rendering it impractical for high-volume environments and applications. We present CellBridge, an automated workflow designed to simplify the standard procedures entailed in scRNA-seq data analysis, eliminating the need for specialized computational expertise. CellBridge utilizes state-of-the-art computational methods, integrating a range of advanced functionalities, covering the entire process from raw unaligned sequencing reads to cell type annotation. Hence, CellBridge accelerates the pace of discovery by seamlessly enabling insights into vast volumes of scRNA-seq data, without compromising workflow control and reproducibility. AVAILABILITY AND IMPLEMENTATION: The source code, detailed documentation, and materials required to reproduce the results are available on GitHub and archived in Zenodo. For the CellBridge pre-processing step (v1.0.0), access the GitHub repository at https://github.com/Sanofi-Public/PMCB-ToBridge and the Zenodo archive at https://zenodo.org/records/10246161. For the CellBridge processing step (v1.0.0), visit the GitHub repository at https://github.com/Sanofi-Public/PMCB-CellBridge and the Zenodo archive at https://zenodo.org/records/10246046.