RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

Shuchao Ren; Yinan Li; Zhipeng Zhou

doi:10.1016/j.jgg.2025.04.010

RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

doi: 10.1016/j.jgg.2025.04.010

National Key Laboratory of Agricultural Microbiology, College of Life Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China

基金项目:

We thank Dr. Yun Zheng and Xiaotuo Zhang for their valuable suggestions and Dr. Jia-Xing Yue for critical reading of the manuscript. We thank Shu Zhou and Daocan Zheng for their constructive feedback. This work is supported by the National Key Research and Development Program of China (2022YFA0912100), the National Natural Science Foundation of China (32270098 and 32470073), the Fundamental Research Funds for the Central Universities (2662024JC015), and the National Key Laboratory of Agricultural Microbiology (AML2024D02) to Z.Z.

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通讯作者:
Zhipeng Zhou,E-mail:zhouzhipeng@mail.hzau.edu.cn

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- 收稿日期: 2024-11-13
- 录用日期: 2025-04-16
- 修回日期: 2025-04-16
- 刊出日期: 2026-01-31

RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

National Key Laboratory of Agricultural Microbiology, College of Life Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China

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摘要

摘要: Translation is a crucial step in gene expression. Over the past decade, the development and application of ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines, improvements in comprehensiveness, accuracy, and user-friendliness are still necessary. In this study, we develop RiboParser/RiboShiny, a robust framework for analyzing and visualizing Ribo-seq data. Building on published methods, we optimize ribosome structure-based and start/stop-based models to improve the accuracy and stability of P-site detection, even in species with a high proportion of leaderless transcripts. Leveraging these improvements, RiboParser offers comprehensive analyses, including quality control, gene-level analysis, codon-level analysis, and the analysis of Ribo-seq variants. Meanwhile, RiboShiny provides a user-friendly and adaptable platform for data visualization, facilitating deeper insights into the translational landscape. Furthermore, the integration of standardized genome annotation renders our platform universally applicable to various organisms with sequenced genomes. This framework has the potential to significantly improve the precision and efficiency of Ribo-seq data interpretation, thereby deepening our understanding of translational regulation.
- Translation /
- Ribosome profiling /
- Ribo-seq /
- Selective Ribo-seq /
- P-site detection /
- Differentially translated genes /
- Translation elongation speed /
- Data visualization
Abstract: Translation is a crucial step in gene expression. Over the past decade, the development and application of ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines, improvements in comprehensiveness, accuracy, and user-friendliness are still necessary. In this study, we develop RiboParser/RiboShiny, a robust framework for analyzing and visualizing Ribo-seq data. Building on published methods, we optimize ribosome structure-based and start/stop-based models to improve the accuracy and stability of P-site detection, even in species with a high proportion of leaderless transcripts. Leveraging these improvements, RiboParser offers comprehensive analyses, including quality control, gene-level analysis, codon-level analysis, and the analysis of Ribo-seq variants. Meanwhile, RiboShiny provides a user-friendly and adaptable platform for data visualization, facilitating deeper insights into the translational landscape. Furthermore, the integration of standardized genome annotation renders our platform universally applicable to various organisms with sequenced genomes. This framework has the potential to significantly improve the precision and efficiency of Ribo-seq data interpretation, thereby deepening our understanding of translational regulation.
- Translation /
- Ribosome profiling /
- Ribo-seq /
- Selective Ribo-seq /
- P-site detection /
- Differentially translated genes /
- Translation elongation speed /
- Data visualization

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参考文献(78)

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RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

doi: 10.1016/j.jgg.2025.04.010

通讯作者:
Zhipeng Zhou,E-mail:zhouzhipeng@mail.hzau.edu.cn

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RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

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RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

doi: 10.1016/j.jgg.2025.04.010

通讯作者: Zhipeng Zhou,E-mail:zhouzhipeng@mail.hzau.edu.cn

计量

出版历程

RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data

计量

出版历程

目录

通讯作者:
Zhipeng Zhou,E-mail:zhouzhipeng@mail.hzau.edu.cn