GitHub - rasilab/subramaniam_cell_2014: Code for Reproduction of Published Figures

Code for Reproducing Analyses and Figures

Reference

Subramaniam AR, Zid B, O’Shea EK. Cell, 159, 1200, 2014

The four IPython Notebooks in this folder are:

sequencing_data_analysis.ipynb — Analysis of high-throughput sequencing data from ribosome profiling and RNA-Seq
simulation.ipynb — E. coli whole-cell translation simulation
simulation_data_analysis.ipynb — Analysis of simulation results. Simulation results can be downloaded from Data Dryad
yeast_simulation_and_analysis.ipynb — Modifications to simulation in Shah et al and analysis of simulation results. Simulation results can be downloaded from Data Dryad

The hyperlinks in the table of contents of each IPython notebook do not seem to be working on github. But they are functional once downloaded locally.
The source code is licensed under GNU GPLv3 license.

Name		Name	Last commit message	Last commit date
README.md		README.md
sequencing_data_analysis.ipynb		sequencing_data_analysis.ipynb
simulation.ipynb		simulation.ipynb
simulation_data_analysis.ipynb		simulation_data_analysis.ipynb
yeast_simulation_and_analysis.ipynb		yeast_simulation_and_analysis.ipynb