OmniClust: A versatile clustering toolkit for single-cell and spatial transcriptomics data.

IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Methods Pub Date : 2025-03-06 DOI:10.1016/j.ymeth.2025.03.007
Yaxuan Cui, Yang Cui, Yi Ding, Kenta Nakai, Leyi Wei, Yuyin Le, Xiucai Ye, Tetsuya Sakurai
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引用次数: 0

Abstract

In recent years, RNA transcriptome sequencing technology has been continuously evolving, ranging from single-cell transcriptomics to spatial transcriptomics. Although these technologies are all based on RNA sequencing, each sequencing technology has its own unique characteristics, and there is an urgent need to develop an algorithmic toolkit that integrates both sequencing techniques. To address this, we have developed OmniClust, a toolkit based on single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data. OmniClust employs deep learning algorithms for feature learning and clustering of spatial transcriptomics data, while utilizing machine learning algorithms for clustering scRNA-seq data. OmniClust was tested on 12 spatial transcriptomics benchmark datasets, demonstrating high clustering accuracy across multiple clustering evaluation metrics. It was also evaluated on four scRNA-seq benchmark datasets, achieving high clustering accuracy based on various clustering evaluation metrics. Furthermore, we applied OmniClust to downstream analyses of spatial transcriptomics and single-cell RNA breast cancer data, showcasing its potential to uncover and interpret the biological significance of cancer transcriptome data. In summary, OmniClust is a clustering tool designed for both single-cell transcriptomics and spatial transcriptomics data, demonstrating outstanding performance.

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来源期刊
Methods
Methods 生物-生化研究方法
CiteScore
9.80
自引率
2.10%
发文量
222
审稿时长
11.3 weeks
期刊介绍: Methods focuses on rapidly developing techniques in the experimental biological and medical sciences. Each topical issue, organized by a guest editor who is an expert in the area covered, consists solely of invited quality articles by specialist authors, many of them reviews. Issues are devoted to specific technical approaches with emphasis on clear detailed descriptions of protocols that allow them to be reproduced easily. The background information provided enables researchers to understand the principles underlying the methods; other helpful sections include comparisons of alternative methods giving the advantages and disadvantages of particular methods, guidance on avoiding potential pitfalls, and suggestions for troubleshooting.
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