SuperSpot: coarse graining spatial transcriptomics data into metaspots.

Bioinformatics (Oxford, England) Pub Date : 2024-12-26 DOI:10.1093/bioinformatics/btae734

Matei Teleman, Aurélie A G Gabriel, Léonard Hérault, David Gfeller

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Abstract

Summary: Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. With current technologies such as VisiumHD, thousands of genes can be detected across millions of spots (also called cells or bins depending on the technologies). Building upon the metacell concept, we present a workflow, called SuperSpot, to combine adjacent and transcriptomically similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptomic similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution. We demonstrate that metaspots reduce the size and sparsity of spatial transcriptomic data and facilitate the analysis of large datasets generated with the most recent technologies.

Availability and implementation: SuperSpot is an R package available at https://github.com/GfellerLab/SuperSpot and archived on Zenodo (https://doi.org/10.5281/zenodo.14222088). The code to reproduce the figures is available at https://github.com/GfellerLab/SuperSpot/tree/main/figures (https://doi.org/10.5281/zenodo.14222088).

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超级斑点：粗粒空间转录组学数据到转移斑点。

摘要：空间转录组学正在彻底改变我们对复杂生物组织进行表型表征和破译细胞生态位的能力。使用目前的技术，如VisiumHD，可以在数百万个点（也称为细胞或箱，取决于技术）中检测到数千个基因。在元细胞概念的基础上，我们提出了一个称为SuperSpot的工作流程，将相邻的和转录相似的点组合成“元点”。该过程包括将点表示为图中的节点，用空间接近的边连接点，边权重表示转录组相似性。分层聚类用于按用户定义的分辨率将点聚合为元点。我们证明，转移点减少了空间转录组数据的大小和稀疏性，并促进了用最新技术生成的大型数据集的分析。可用性和实现：SuperSpot是一个R包，可从https://github.com/GfellerLab/SuperSpot获得，并存档于Zenodo （https://doi.org/10.5281/zenodo.14222088）。复制这些数字的代码可在https://github.com/GfellerLab/SuperSpot/tree/main/figures (https://doi.org/10.5281/zenodo.14222088).Supplementary信息：补充数据可在Bioinformatics在线获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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