Regional analysis to delineate intrasample heterogeneity with RegionalST.
Regional analysis to delineate intrasample heterogeneity with RegionalST.
复制标题
使用 RegionalST 描述样本内异质性的区域分析。
DOI：
10.1093/bioinformatics/btae186
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发表时间：
2024
期刊：
影响因子：
--
通讯作者：
Li,Ziyi
中科院分区：
文献类型：
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作者：
Lyu,Yue;Wu,Chong;Sun,Wei;Li,Ziyi
空间转录组学极大地促进了我们对空间和样本内异质性的理解，这对于破译人类疾病的分子基础至关重要。肿瘤内异质性，例如，可能与癌症治疗反应相关。然而，缺乏计算工具，利用跨区域的信息和有限的空间分辨率，目前的技术提出的主要障碍，阐明组织heterogeneity.ResultsTo解决这些挑战，我们介绍RegionalST，一种有效的计算方法，使用户能够量化细胞类型的混合物和相互作用，确定感兴趣的子区域，首次进行跨区域细胞类型特异性差异分析。我们的模拟和真实的数据应用表明，RegionalST是一种有效的工具，用于可视化和分析不同的空间转录组学数据，从而实现准确和灵活的探索组织异质性。总体而言，RegionalST为寻求深入研究空间转录组学数据的复杂性的研究人员提供了一站式目的地。可用性和实施我们的方法的实施可作为开源R/Bioconductor包，并在https://bioconductor.org/packages/release/bioc/html/RegionalST.html上提供用户友好的手册。
MotivationSpatial transcriptomics has greatly contributed to our understanding of spatial and intra-sample heterogeneity, which could be crucial for deciphering the molecular basis of human diseases. Intra-tumor heterogeneity, e.g. may be associated with cancer treatment responses. However, the lack of computational tools for exploiting cross-regional information and the limited spatial resolution of current technologies present major obstacles to elucidating tissue heterogeneity.ResultsTo address these challenges, we introduce RegionalST, an efficient computational method that enables users to quantify cell type mixture and interactions, identify sub-regions of interest, and perform cross-region cell type-specific differential analysis for the first time. Our simulations and real data applications demonstrate that RegionalST is an efficient tool for visualizing and analyzing diverse spatial transcriptomics data, thereby enabling accurate and flexible exploration of tissue heterogeneity. Overall, RegionalST provides a one-stop destination for researchers seeking to delve deeper into the intricacies of spatial transcriptomics data.Availability and implementationThe implementation of our method is available as an open-source R/Bioconductor package with a user-friendly manual available at https://bioconductor.org/packages/release/bioc/html/RegionalST.html.