BatchSVG: identifying batch-biased genes in the application of spatially variable gene detection.

ABSTRACT: A standard task in the analysis of spatially resolved transcriptomics data is to identify spatially variable genes (SVGs). This is most commonly done within one tissue section at a time because the spatial relationships between the tissue sections are typically unknown. However, large-scale spatial atlases are being generated, for example across hundreds of donors, where the goal is to identify a common set of SVGs to use for downstream analyses. One challenge is how to identify and remove SVGs that are associated with a known bias or technical artifact, such as the slide or capture area, which can lead to poor performance in downstream analyses, such as spatial domain detection. Here, we introduce BatchSVG, a tool to identify batch-biased genes in the application of SVG detection. Our app

SUBMITTER: Shah K 

PROVIDER: S-EPMC12713593 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature