riboHMM2 is an R package designed to find the locations of upstream Open Reading Frames (uORFs) and the main coding region in RNA.
Given the ribo-seq counts, one can use riboHMM2 to estimate the parameters in the assumed hidden Markov model, and further to predict the the locations of uORFs and the main coding region in RNA.
Start R and run:
library(devtools)
install_github("shimlab/riboHMM2")
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