ArticleComputational and structural biotechnology journal2021
RiboDoc: A Docker-based package for ribosome profiling analysis.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Divergent proteome tolerance against gain and loss of chromosome arms.Molecular cell · 2025Article
- Transcriptome Analysis Reveals the Role of Plant Hormone Signal Transduction Pathways in the Drought Stress Response ofPlants (Basel, Switzerland) · 2025Article
- Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.Nature communications · 2025Article
- Aminoglycoside tolerance ineLife · 2025Article
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis.The Plant cell · 2024Article
- Next generation sequencing technologies to address aberrant mRNA translation in cancer.NAR cancer · 2024Review
- Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.Wellcome open research · 2024Article
- Translatomics to explore dynamic differences in immunocytes in the tumor microenvironment.Molecular therapy. Nucleic acids · 2023Review
- 2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here (https://github.com/equipeGST/RiboDoc), we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.
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