iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks.

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2021-02-18 DOI:10.1186/s13059-021-02280-8
Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang
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Abstract

The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsupervised batch effect removal framework, called iMAP, based on both deep autoencoders and generative adversarial networks. Compared with current methods, iMAP shows superior, robust, and scalable performance in terms of both reliably detecting the batch-specific cells and effectively mixing distributions of the batch-shared cell types. Applying iMAP to tumor microenvironment datasets from two platforms, Smart-seq2 and 10x Genomics, we find that iMAP can leverage the powers of both platforms to discover novel cell-cell interactions.

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iMAP:通过对抗性配对转移网络整合多个单细胞数据集。
整合来自多个来源的单细胞 RNA 序列数据集对于破译复杂生物系统中细胞间的异质性和相互作用至关重要。我们基于深度自动编码器和生成式对抗网络,提出了一种新颖的无监督批量效应去除框架,称为 iMAP。与目前的方法相比,iMAP 在可靠地检测批特异性细胞和有效地混合批共享细胞类型的分布方面都表现出卓越、稳健和可扩展的性能。将 iMAP 应用于来自 Smart-seq2 和 10x Genomics 这两个平台的肿瘤微环境数据集,我们发现 iMAP 可以利用这两个平台的优势发现新的细胞-细胞相互作用。
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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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