SNPmanifold:检测单细胞克隆和谱系从单核苷酸变异使用二项变分自编码器

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Hoi Man Chung, Yuanhua Huang
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引用次数: 0

摘要

高协方差单细胞谱系追踪数据的单核苷酸变异(SNV)克隆分配仍然是一个挑战,因为分层突变结构和许多缺失信号。我们开发了SNPmanifold,这是一个Python包,它使用二项式变分自编码器学习SNV嵌入流形,以给出有效且可解释的细胞-细胞距离度量。我们证明SNPmanifold是一种适合分析复杂的单细胞SNV突变数据的工具,例如在通过线粒体SNV数据进行大量供体解路和体细胞谱系追踪的背景下,可以比现有方法更准确和全面地揭示单细胞克隆和谱系。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder
Single-nucleotide-variant (SNV) clone assignment of high-covariance single-cell lineage tracing data remains a challenge due to hierarchical mutation structure and many missing signals. We develop SNPmanifold, a Python package that learns an SNV embedding manifold using a binomial variational autoencoder to give an efficient and interpretable cell-cell distance metric. We demonstrate that SNPmanifold is a suitable tool for analysis of complex, single-cell SNV mutation data, such as in the context of demultiplexing a large number of donors and somatic lineage tracing via mitochondrial SNV data and can reveal insights into single-cell clonality and lineages more accurately and comprehensively than existing methods.
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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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