Here are the R code for analyzing the Ribo-seq, RiboTaper and dual-luciferase assay results.
A. RiboTaper for Arabidopsis 7-day old seedling data (including Bowtie2, Stringtie, gffcompare, STAR/RSEM/RiboTaper steps and associated R code for analysis) B1. Identification of minimum uORFs with CiPS
B2: Identification of other uORFs with CiPS
C. Identification of uORFs that overlap with each other
D. Identification of uORFs that are regulated by alternative splicing in our experimental conditions
E. Cumulative plot and multiple comparison Kolmogorov–Smirnov test
F. Box plot and Wilcoxon rank-sum test

RNA-seq and Ribo-seq data: Here under accession number: GSE183264 The gtf and other files required for this analysis is available Here
For visualizing individual genes, please use RiboPlotR