ORF-RATER (Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
The software was created at Jonathan Weissman's lab at UCSF and is described in Fields, Rodriguez, et al., "A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation", Molecular Cell 60, 816-827 (2015).
Usage information can be found in the Detailed Protocol included in the paper's supplemental materials, or by running each script with the --help/-h flag.
Required packages include numpy, scipy, pysam, biopython, pandas, scikit-learn, pybedtools, and plastid, all of which are available through PyPI.
Some features require the multiisotonic package, which must be downloaded manually.
Contact Alex Fields for further information or assistance.