Dataset Information

SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data.

ABSTRACT: In high-throughput spatial transcriptomics (ST) studies, it is of great interest to identify the genes whose level of expression in a tissue covaries with the spatial location of cells/spots. Such genes, also known as spatially variable genes (SVGs), can be crucial to the biological understanding of both structural and functional characteristics of complex tissues. Existing methods for detecting SVGs either suffer from huge computational demand or significantly lack statistical power. We propose a non-parametric method termed SMASH that achieves a balance between the above two problems. We compare SMASH with other existing methods in varying simulation scenarios demonstrating its superior statistical power and robustness. We apply the method to four ST datasets from different platforms revealing interesting biological insights.

SUBMITTER: Seal S

PROVIDER: S-EPMC10055313 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data.

Seal Souvik S Bitler Benjamin G BG Ghosh Debashis D

bioRxiv : the preprint server for biology 20230330

In high-throughput spatial transcriptomics (ST) studies, it is of great interest to identify the genes whose level of expression in a tissue covaries with the spatial location of cells/spots. Such genes, also known as spatially variable genes (SVGs), can be crucial to the biological understanding of both structural and functional characteristics of complex tissues. Existing methods for detecting SVGs either suffer from huge computational demand or significantly lack statistical power. We propose ...[more]

PMID: 36993287

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Dataset Information

SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data.

Publications

SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data.

Similar Datasets

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