利用 concordex 识别组织中的空间均质区域。

IF 2.1 3区工程技术 Q3 ENGINEERING, ELECTRICAL & ELECTRONIC

IEEE Transactions on Magnetics Pub Date : 2024-07-18 DOI:10.1101/2023.06.28.546949

Kayla C Jackson, A Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Lior Pachter

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引用次数: 0

摘要

组织中的空间均质区（SHR）是指细胞类型组成均一的区域。我们提出了一种利用空间转录组学数据识别 SHRs 的方法，并证明该方法能高效、有效地为多种组织类型找到 SHRs。该方法是在一个名为 concordex 的工具中实现的，它依赖于对 k-近邻（kNN）图的分析。concordex 工具还可用于分析非空间转录组学数据，并能阐明聚类算法得出的细胞分区与 kNN 图所代表的转录组相似性之间的一致程度。

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Identification of spatial homogeneous regions in tissues with concordex.

Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. The method is implemented in a tool called concordex, which relies on analysis of k-nearest-neighbor (kNN) graphs. The concordex tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.

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来源期刊

IEEE Transactions on Magnetics 工程技术-工程：电子与电气

CiteScore

4.00

自引率

14.30%

发文量

565

审稿时长

4.1 months

期刊介绍： Science and technology related to the basic physics and engineering of magnetism, magnetic materials, applied magnetics, magnetic devices, and magnetic data storage. The IEEE Transactions on Magnetics publishes scholarly articles of archival value as well as tutorial expositions and critical reviews of classical subjects and topics of current interest.