ggRibo : a ggplot-based single-gene viewer for visualizing Ribo-seq and related omics datasets

Visualizing periodic Ribo-seq data within genes of interest is a powerful approach to studying mRNA translation, but its application is limited by a lack of robust tools. Here, we introduce ggRibo , a user-friendly R package for visualizing individual gene expression, integrating Ribo-seq, RNA-seq, and other genome-wide datasets with flexible scaling options. ggRibo presents the 3-nucleotide periodicity, a hallmark of translating ribosomes, within a gene-structure context, including introns and untranslated regions, enabling the study of novel ORFs, isoform translation, and mechanisms of translational regulation. ggRibo can plot multiple Ribo-seq/RNA-seq datasets from different conditions for comparison. Additionally, it supports the visualization of other omics datasets that could also be presented with single-nucleotide resolution, such as RNA degradome, transcription start sites, and translation initiation sites. Through its intuitive and flexible platform, ggRibo enables parallel comparisons of multi-omic datasets, facilitating a comprehensive understanding of gene expression regulation and promoting hypothesis generation. We demonstrate its utility with examples of upstream ORFs, downstream ORFs, isoform translation, and multi-omic comparison in humans and Arabidopsis. In summary, ggRibo is an advanced single-gene viewer that enhances the interpretation of translatome and related genome-wide datasets, offering a valuable resource for studying gene expression regulation. ggRibo is available on GitHub ( https://github.com/hsinyenwu/ggRibo ).