ArticleBioinformatics (Oxford, England)2020
RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells.bioRxiv : the preprint server for biology · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- Developmental and transcriptional programs that define the initiation of the forelimb.Development (Cambridge, England) · 2026Article
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Ribosome Molecular Aging Shapes Translation Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Translational buffering tunes gene expression in mice and humans.Genome biology · 2026Article
- Cycloheximide-resistant ribosomes reveal adaptive translation dynamics in C. elegans.Genetics · 2026Article
- A Versatile Ribo-seq Workflow for Enhanced Analysis of Ribosome Dynamics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Developmental and transcriptional programs that define the initiation of the forelimb.bioRxiv : the preprint server for biology · 2025Article
- Topological and functional characterization of human translation efficiency covariation network.Bioinformatics (Oxford, England) · 2025Article
- ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data.bioRxiv : the preprint server for biology · 2025Article
- A programmed decline in ribosome levels governs human early neurodevelopment.Nature cell biology · 2025Article
- Landscape and regulation of mRNA translation in the early C. elegans embryo.Cell reports · 2025Article
- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- Landscape and regulation of mRNA translation in the earlybioRxiv : the preprint server for biology · 2025Article
- Differential impacts of ribosomal protein haploinsufficiency on mitochondrial function.The Journal of cell biology · 2025Article
- The assembly factor Reh1 is released from the ribosome during its initial round of translation.Nature communications · 2025Article
- Ribo-ITP: A Method for Ribosome Profiling in Single Cells and Low-Input Samples.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
summaryRibosome occupancy measurements enable protein abundance estimation and infer mechanisms of translation. Recent studies have revealed that sequence read lengths in ribosome profiling data are highly variable and carry critical information. Consequently, data analyses require the computation and storage of multiple metrics for a wide range of ribosome footprint lengths. We developed a software ecosystem including a new efficient binary file format named 'ribo'. Ribo files store all essential data grouped by ribosome footprint lengths. Users can assemble ribo files using our RiboFlow pipeline that processes raw ribosomal profiling sequencing data. RiboFlow is highly portable and customizable across a large number of computational environments with built-in capabilities for parallelization. We also developed interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments. Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots and carry out analyses. Altogether, these components create a software ecosystem for researchers to study translation through ribosome profiling. AVAILABILITY AND IMPLEMENTATION: For a quickstart, please see https://ribosomeprofiling.github.io. Source code, installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.