SMaSH: A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics

Nelson, M. E.; Riva, S. G.; Cvejic, A.

doi:10.1101/2021.04.08.438978

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bioRxiv · 10.1101/2021.04.08.438978

SMaSH: A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics

Nelson, M. E.·Riva, S. G.·Cvejic, A.

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Abstract

Spatial transcriptomics is revolutionising the study of single-cell RNA and tissue-wide cell heterogeneity, but few robust methods connecting spatially resolved cells to so-called marker genes from single-cell RNA sequencing, which generate significant insight gleaned from spatial methods, exist. Here we present SMaSH, a general computational framework for extracting key marker genes from single-cell RNA sequencing data for spatial transcriptomics approaches. SMaSH extracts robust and biologically well-motivated marker genes, which characterise the given data-set better than existing and limited computational approaches for global marker gene calculation.

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Nelson, M. E., Riva, S. G., Cvejic, A.. 2021-04-09. SMaSH: A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics. https://doi.org/10.1101/2021.04.08.438978

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