LVPT: Lazy Velocity Pseudotime Inference Method
The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological t...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-08-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/8/1242 |
| _version_ | 1797585397722644480 |
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| author | Shuainan Mao Jiajia Liu Weiling Zhao Xiaobo Zhou |
| author_facet | Shuainan Mao Jiajia Liu Weiling Zhao Xiaobo Zhou |
| author_sort | Shuainan Mao |
| collection | DOAJ |
| description | The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of pseudotime inference compared with other existing methods on both simulated datasets with different structures and real datasets. The validation results were consistent with prior knowledge, indicating that LVPT is an accurate and efficient method for pseudotime inference. |
| first_indexed | 2024-03-11T00:05:35Z |
| format | Article |
| id | doaj.art-93684fc864ed431ebd7623805585e963 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T00:05:35Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-93684fc864ed431ebd7623805585e9632023-11-19T00:24:12ZengMDPI AGBiomolecules2218-273X2023-08-01138124210.3390/biom13081242LVPT: Lazy Velocity Pseudotime Inference MethodShuainan Mao0Jiajia Liu1Weiling Zhao2Xiaobo Zhou3The Department of Biotherapy and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, ChinaCenter for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USACenter for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USACenter for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USAThe emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of pseudotime inference compared with other existing methods on both simulated datasets with different structures and real datasets. The validation results were consistent with prior knowledge, indicating that LVPT is an accurate and efficient method for pseudotime inference.https://www.mdpi.com/2218-273X/13/8/1242single celltrajectory inferencepseudotime inferencerandom walk |
| spellingShingle | Shuainan Mao Jiajia Liu Weiling Zhao Xiaobo Zhou LVPT: Lazy Velocity Pseudotime Inference Method Biomolecules single cell trajectory inference pseudotime inference random walk |
| title | LVPT: Lazy Velocity Pseudotime Inference Method |
| title_full | LVPT: Lazy Velocity Pseudotime Inference Method |
| title_fullStr | LVPT: Lazy Velocity Pseudotime Inference Method |
| title_full_unstemmed | LVPT: Lazy Velocity Pseudotime Inference Method |
| title_short | LVPT: Lazy Velocity Pseudotime Inference Method |
| title_sort | lvpt lazy velocity pseudotime inference method |
| topic | single cell trajectory inference pseudotime inference random walk |
| url | https://www.mdpi.com/2218-273X/13/8/1242 |
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