tTEscanR: A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems

Abstract

Translation elongation relies on accurate codon-anticodon pairing. Here, we present tTEscanR, an R package designed to investigate this translational interface. By quantifying mRNA codon demand alongside tRNA anticodon availability, tTEscanR provides scalable estimates of translation rates directly from standard transcriptomic and chromatin accessibility count matrices, where genomic features are represented as rows and experimental conditions as columns. tTEscanR seamlessly integrates into existing bulk and single-cell pipelines and provides modular functions for quality control, filtering, normalization, statistical analysis, and visualization. A structured data object centralizes workflow outputs and associated metadata. A built-in multilevel visualization module generates customizable, publication-ready graphical outputs to facilitate data interpretation and reproducibility of the complex translational landscape. We demonstrate the utility of tTEscanR across cancer biology, aging, and neurodegeneration datasets, uncovering critical translational regulatory programs overlooked by conventional analyses. tTEscanR is available in an open-source repository as a standalone tool or workflow plug-in.