EuroBioC 2025 Workshop: OSTA - Orchestrating Spatial Omics Analysis with Bioconductor

Описание: OSTA: Orchestrating Spatial (Transcript-)Omics Analysis with Bioconductor

Author(s): Yixing Dong & Ellis Patrick: Auditorium

Spatial omics technologies have advanced rapidly over the past five years, spanning both sequencing-based and imaging-based platforms, with applications across diverse tissues such as the brain and cancer. However, despite these technological leaps, many current analysis pipelines have been adapted from single-cell RNA-seq workflows without sufficient tailoring to the unique spatial context. As a result, a comprehensive, statistically-informed framework for spatial transcriptomics analysis remains largely absent. To address this gap, we have collaboratively developed an open-source online book that serves as the most comprehensive Bioconductor-based resource for spatial transcriptomics to date (https://lmweber.org/OSTA/). This book offers step-by-step tutorials built around publicly available datasets, covering a broad spectrum of spatial technologies and resolutions, from Visium, Visium HD, to Xenium and CosMx. We showcase workflows that incorporate spatial statistical methods for pattern detection, modeling spatial variability, and integrating multimodal data. Our resource also emphasizes reproducibility and interoperability between R and Python data classes and tools. In this workshop, we will present newly developed workflow chapters that establish various avenues of spatial omics data analysis. We will also demonstrate complete pipelines—from raw data ingestion to spatial visualization and biological interpretation—designed to be both user-friendly and extensible to emerging technologies. By promoting open standards and cross-language compatibility, our work aims to equip the spatial omics community with reproducible, robust, and accessible analytical tools.