stPipe: A flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data

Spatial transcriptomics technology has developed rapidly in recent years, with various sequencing-based platforms such as 10x Visium, Slide-seq and Stereo-seq becoming widely used by researchers. Each platform brings its own set of protocols and customised data analysis pipelines which presents challenges when the goal is to obtain uniformly preprocessed data that is conveniently formatted for downstream analysis. To address the need for simpler, open-source solutions that deal with sequencing-based spatial transcriptomics (sST) data from different platforms, we present stPipe, a comprehensive and modular pipeline for analysing sST data. stPipe handles various analysis steps including (i) data processing from raw paired end FASTQ files to create a spatially resolved gene count matrix; (ii) the collation of relevant quality control metrics during preprocessing to ensure unwanted artefacts can be filtered from further analysis; and (iii) the adoption of standardised data storage containers to allow results to be easily passed on to a wide range of downstream analysis packages tailored to different goals (such as clustering, cell-cell communication analysis and differential expression analysis). stPipe is implemented as an R/Bioconductor package that builds upon functionality in the scPipe software, and offers a flexible preprocessing pipeline that can manage data from all current main-stream sST plaforms. A key use case for stPipe is in methods benchmarking, and we demonstrate how the uniform processing of sST data collected on reference tissue samples from the cadasSTre and SpatialBenchVisium projects is made easier, allowing comparisons between different technology platforms and downstream analysis tools. Our framework thus aims to advance the standardization and optimization of spatial transcriptomics analyses, fostering collaboration and innovation within the research community.