GxP Single-cell RNA-seq and Spatial Transcriptomics end-to-end pipeline for clinical research

Single-cell/nucleus RNA-sequencing and Spatial Transcriptomics are powerful tools for investigating cellular heterogeneity and tissue architecture that have deepened our disease understanding. Their broader adoption in clinical and regulated settings, however, is hindered by challenges related to data integrity, regulatory compliance, reproducibility, and scalability. To address this gap, we developed NNclinSSOAP (Novo Nordisk Clinical Single-cell Spatial Omics Analytical Pipeline) - a modular, GxP-ready end-to-end computational pipeline, that combines established single-cell workflows with a new Nextflow pipeline for Spatial Transcriptomics. NNclinSSOAP transforms RNA sequencing and Xenium spatial data into integrated, annotated single-cell objects and spatially resolved tissue maps. Designed to support mechanistic studies and clinical endpoint generation, it enables traceable and reproducible processing of large-scale datasets, scalable for both local and HPC environments. Here, we provide a step-by-step guide for using NNclinSSOAP. All code and data are publicly available. Using a standard laptop, the pipeline can be executed within 1.5 hours.