The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation

Additional files, Scripts and Data related to the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. 

Additional file 1: contains supplemental figures and tables of the manuscript

Additional file 2: contains the complete list of the 89 Ribo-Seq datasets (89 biological replicas).

Papadopoulos_et_al_2024.tar.gz: contains the scripts, raw data, intermediate data and final (processed) data to reproduce the analyses, Figures, and Tables of the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. 

The archive contains 3 directories:

*** input: contains the protocols, raw data, and the associated intermediate processed data that are used as inputs of the scripts that perform the subsequent analyses and generate the Figures and Tables

*** scripts: all the scripts necessary to perform the analyses of the manuscript and generate the final data, Figures and Tables available in the ./output directory

*** output: contains the final processed data including the final lists and tables resulting from MSMS analyses or RiboSeq analyses, the final Figures and Tables of the manuscript     as well as the 3 final tables that integrate the processed data from Ribo-Seq, MSMS, evolutionary analyses, sequence and structural analyses, final analyses on codon propensities. These 3 tables, beyond being necessary for the anlayses performed for this study can also be useful for users to realize their own analyses. All the data, Figures and Tables contained in this directory can be directly generated from the scripts available in the directory ./scripts and the data contained in the directory ./input. Please see the README in the different directories to reproduce everything.