carinelegrand/RiboVIEW: Visualization, Quality and Statistics for Ribosome Profiling

Ribosomes translate messenger RNAs (mRNAs) into proteins, and ribosome profiling technique allows to retrieve those mRNAs fragments which are under active translation in a ribosome. These mRNA fragments are then generally sequenced and further analysed for codon enrichment, translation efficiency, etc. In this package we provide tools to compute and visualize results, perform quality control, and derive an unbiased estimate of codon enrichment. We offer the user a webpage view to scan own data on the following aspects: periodicity, ligation and digestion of ribosome-protected footprints; reproducibility and batch effects of replicates; drugs-related artifacts; codon enrichment including variability observed between mRNAs and positions for ribosome acceptor, peptidyl and exit (A, P and E, respectively) sites ; mining of causal or confounding factors. Reference : Legrand, C. and Tuorto, F. (in press) RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data, Nucleic Acids Research, doi : 10.1093/nar/gkz1074. (URL of advance article, online 28.11.2019 : https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1074/5645003)

install.packages("remotes")
remotes::install_github("carinelegrand/RiboVIEW")