SpatialOne: End-to-End analysis of visium data at scale.

Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of methods and libraries required for that purpose. Here we present SpatialOne, an end-to-end pipeline designed to simplify the analysis of 10x Visium data by combining multiple state-of-the-art computational methods to segment, deconvolve and quantify spatial information; this approach streamlines the analysis of reproducible spatial-data at scale. SpatialOne source code and execution examples are available at https://github.com/Sanofi-Public/spatialone-pipeline. SpatialOne is distributed as a docker container image. Supplementary data are available at Bioinformatics online.

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© The Author(s) 2024. Published by Oxford University Press.