GraphPCA: a fast and interpretable dimension reduction algorithm for spatial transcriptomics data

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Genome Biology Pub Date : 2024-11-07 DOI:10.1186/s13059-024-03429-x
Jiyuan Yang, Lu Wang, Lin Liu, Xiaoqi Zheng
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Abstract

The rapid advancement of spatial transcriptomics technologies has revolutionized our understanding of cell heterogeneity and intricate spatial structures within tissues and organs. However, the high dimensionality and noise in spatial transcriptomic data present significant challenges for downstream data analyses. Here, we develop GraphPCA, an interpretable and quasi-linear dimension reduction algorithm that leverages the strengths of graphical regularization and principal component analysis. Comprehensive evaluations on simulated and multi-resolution spatial transcriptomic datasets generated from various platforms demonstrate the capacity of GraphPCA to enhance downstream analysis tasks including spatial domain detection, denoising, and trajectory inference compared to other state-of-the-art methods.
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GraphPCA:用于空间转录组学数据的快速、可解释的降维算法
空间转录组学技术的快速发展彻底改变了我们对细胞异质性以及组织和器官内复杂空间结构的认识。然而,空间转录组数据的高维度和噪声给下游数据分析带来了巨大挑战。在此,我们开发了 GraphPCA,这是一种可解释的准线性降维算法,充分利用了图形正则化和主成分分析的优势。通过对各种平台生成的模拟和多分辨率空间转录组数据集进行全面评估,证明与其他最先进的方法相比,GraphPCA 有能力增强下游分析任务,包括空间域检测、去噪和轨迹推断。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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