-
Notifications
You must be signed in to change notification settings - Fork 1
carinelegrand/RiboVIEW
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
This is package RiboVIEW for Visualization, Quality and Statistics for Ribosome Profiling Purpose : 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) Installation : From R, install devtools package if you don't already have it installed : install.packages("devtools") Then, import the just installed library : library(devtools) Finally, install RiboVIEW from its github repositery : install_github("carinelegrand/RiboVIEW")
About
Visualization, Quality and Statistics for Ribosome Profiling
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published