Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data Article Swipe
Zhaoyang Huang
,
Xinyang Guo
,
Jie Qin
,
Lin Gao
,
Fen Ju
,
Chenguang Zhao
,
Liang Yu
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1186/s12915-024-02085-8
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1186/s12915-024-02085-8
RNA velocity, as an extension of trajectory inference, is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. However, existing RNA velocity methods are limited by the batch effect because they cannot directly correct for batch effects in the input data, which comprises spliced and unspliced matrices in a proportional relationship. This limitation can lead to an incorrect velocity stream. This paper introduces VeloVGI, which addresses this issue innovatively in two key ways. Firstly, it employs an optimal transport (OT) and mutual nearest neighbor (MNN) approach to construct neighbors in batch data. This strategy overcomes the limitations of existing methods that are affected by the batch effect. Secondly, VeloVGI improves upon VeloVI's velocity estimation by incorporating the graph structure into the encoder for more effective feature extraction. The effectiveness of VeloVGI is demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb tissue, as well as on several public datasets. The results show that VeloVGI outperformed other methods in terms of metric performance.
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1186/s12915-024-02085-8
- https://bmcbiol.biomedcentral.com/counter/pdf/10.1186/s12915-024-02085-8
- OA Status
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- Cited By
- 19
- References
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- Related Works
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- OpenAlex ID
- https://openalex.org/W4405525278
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- OpenAlex ID
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https://openalex.org/W4405525278Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1186/s12915-024-02085-8Digital Object Identifier
- Title
-
Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq dataWork title
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-12-18Full publication date if available
- Authors
-
Zhaoyang Huang, Xinyang Guo, Jie Qin, Lin Gao, Fen Ju, Chenguang Zhao, Liang YuList of authors in order
- Landing page
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https://doi.org/10.1186/s12915-024-02085-8Publisher landing page
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https://bmcbiol.biomedcentral.com/counter/pdf/10.1186/s12915-024-02085-8Direct link to full text PDF
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goldOpen access status per OpenAlex
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https://bmcbiol.biomedcentral.com/counter/pdf/10.1186/s12915-024-02085-8Direct OA link when available
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Biology, Inference, RNA, Encoder, Data mining, Computer science, Pattern recognition (psychology), Artificial intelligence, Gene, Genetics, Operating systemTop concepts (fields/topics) attached by OpenAlex
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19Total citation count in OpenAlex
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2025: 19Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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