利用 concordex 识别组织中的空间均质区域。

IF 1.9 3区 工程技术 Q3 ENGINEERING, ELECTRICAL & ELECTRONIC
Kayla C Jackson, A Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Alexandra Kim, Orhan Hosten-Mittermaier, 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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Characterization of spatial homogeneous regions in tissues with concordex.

The rapid advancement of spatially resolved transcriptomics (SRT) technologies has facilitated exploration of how gene expression varies across tissues. However, identifying spatially variable genes remains challenging due to confounding variation introduced by the spatial distribution of cell types. We introduce a new approach to identifying spatial domains that are homogeneous with respect to cell-type composition that facilitates the decomposition of gene expression patterns by cell-type and spatial variation. Our method, called concordex, is efficient and effective across technological platforms and tissue types, and using several biological datasets we show that it can be used to identify genes with subtle variation patterns that are missed when considering only cell-type variation, or spatial variation, alone. The concordex tool is freely available at https://github.com/pachterlab/concordexR.

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来源期刊
IEEE Transactions on Magnetics
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.
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