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bioRxiv · 10.1101/2019.12.11.872895

SingleCellSignalR: Inference of intercellular networks from single-cell transcriptomics

Cabello-Aguilar, S.·Kon Sun Tack, F.·Alame, M.·Fau, C.·Lacroix, M.·Colinge, J.
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Abstract

Single-cell transcriptomics offers unprecedented opportunities to infer the ligand-receptor interactions underlying cellular networks. We introduce a new, curated ligand-receptor database and a novel regularized score to perform such inferences. For the first time, we try to assess the confidence in predicted ligand-receptor interactions and show that our regularized score outperforms other scoring schemes while controlling false positives. SingleCellSignalR is implemented as an open-access R package accessible to entry-level users and available from https://github.com/SCA-IRCM. Analysis results come in a variety of tabular and graphical formats. For instance, we provide a unique network view integrating all the intercellular interactions, and a function relating receptors to expressed intracellular pathways. A detailed comparison with related tools is conducted. Among various examples, we demonstrate SingleCellSignalR on mouse epidermis data and discover an oriented communication structure from external to basal layers.

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Cabello-Aguilar, S., Kon Sun Tack, F., Alame, M., Fau, C., Lacroix, M., Colinge, J.. 2019-12-12. SingleCellSignalR: Inference of intercellular networks from single-cell transcriptomics. https://doi.org/10.1101/2019.12.11.872895

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