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bioRxiv · 10.1101/2023.09.19.558514

InSituCor: a toolkit for discovering non-trivial spatial correlations in spatial transcriptomics

Danaher, P.·McGuire, D.·Patrick, M.·Kroeppler, D.·Zhai, H.·Schmid, J.·Beechem, J. M.
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Abstract

Spatial transcriptomics presents the best kind of problem: how to find the many biological insights hidden within complex datasets. Spatially correlated genes can reveal high-interest phenomena like cell-cell interactions and latent variables. We introduce InSituCor, a toolkit for discovering modules of spatially correlated genes. A major contribution is that InSituCor returns only correlations not explainable by obvious factors like the cell type landscape; this spares precious analyst effort for non-trivial findings. InSituCor supports both unbiased discovery of whole-dataset correlations and knowledge-driven exploration of genes of interest. As a special case, it evaluates ligand-receptor pairs for spatial co-regulation.

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Danaher, P., McGuire, D., Patrick, M., Kroeppler, D., Zhai, H., Schmid, J., Beechem, J. M.. 2023-09-22. InSituCor: a toolkit for discovering non-trivial spatial correlations in spatial transcriptomics. https://doi.org/10.1101/2023.09.19.558514

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