M3S : a comprehensive model selection for multi-modal single-cell RNA sequencing data
BACKGROUND: Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data generated by different experimental design and platforms, there is currently lack of capability to determine the most proper statistical model.
RESULTS: We developed an R package, namely Multi-Modal Model Selection (M3S), for gene-wise selection of the most proper multi-modality statistical model and downstream analysis, useful in a single-cell or large scale bulk tissue transcriptomic data. M3S is featured with (1) gene-wise selection of the most parsimonious model among 11 most commonly utilized ones, that can best fit the expression distribution of the gene, (2) parameter estimation of a selected model, and (3) differential gene expression test based on the selected model.
CONCLUSION: A comprehensive evaluation suggested that M3S can accurately capture the multimodality on simulated and real single cell data. An open source package and is available through GitHub at https://github.com/zy26/M3S.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2019 |
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| Erschienen: |
2019 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:20 |
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| Enthalten in: |
BMC bioinformatics - 20(2019), Suppl 24 vom: 20. Dez., Seite 672 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zhang, Yu [VerfasserIn] |
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| Links: |
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| Themen: |
63231-63-0 |
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| Anmerkungen: |
Date Completed 25.03.2020 Date Revised 25.03.2020 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1186/s12859-019-3243-1 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM304624616 |
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| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a BACKGROUND: Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data generated by different experimental design and platforms, there is currently lack of capability to determine the most proper statistical model | ||
| 520 | |a RESULTS: We developed an R package, namely Multi-Modal Model Selection (M3S), for gene-wise selection of the most proper multi-modality statistical model and downstream analysis, useful in a single-cell or large scale bulk tissue transcriptomic data. M3S is featured with (1) gene-wise selection of the most parsimonious model among 11 most commonly utilized ones, that can best fit the expression distribution of the gene, (2) parameter estimation of a selected model, and (3) differential gene expression test based on the selected model | ||
| 520 | |a CONCLUSION: A comprehensive evaluation suggested that M3S can accurately capture the multimodality on simulated and real single cell data. An open source package and is available through GitHub at https://github.com/zy26/M3S | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Differential gene expression analysis | |
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| 650 | 4 | |a Left truncated mixture Gaussian | |
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| 650 | 4 | |a Single cell RNA-seq | |
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| 700 | 1 | |a Wan, Changlin |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Pengcheng |e verfasserin |4 aut | |
| 700 | 1 | |a Chang, Wennan |e verfasserin |4 aut | |
| 700 | 1 | |a Huo, Yan |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Jian |e verfasserin |4 aut | |
| 700 | 1 | |a Ma, Qin |e verfasserin |4 aut | |
| 700 | 1 | |a Cao, Sha |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Chi |e verfasserin |4 aut | |
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