ArticleBioinformatics (Oxford, England)2024
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- 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
- Translational buffering tunes gene expression in mice and humans.Genome biology · 2026Article
- Cycloheximide-resistant ribosomes reveal adaptive translation dynamics in C. elegans.Genetics · 2026Article
- Developmental and transcriptional programs that define the initiation of the forelimb.bioRxiv : the preprint server for biology · 2025Article
- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- The assembly factor Reh1 is released from the ribosome during its initial round of translation.Nature communications · 2025Article
- Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.Wellcome open research · 2024Article
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3 authors.
Funding
Abstract
motivationRibosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses.
resultsIn this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data. AVAILABILITY AND IMPLEMENTATION: Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.
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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.