Code for Reproduction of Published Figures
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README.md
sequencing_data_analysis.ipynb
simulation.ipynb
simulation_data_analysis.ipynb
yeast_simulation_and_analysis.ipynb

README.md

Code for Reproducing Analyses and Figures

Reference

An integrated approach reveals regulatory controls on bacterial translation elongation

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

The four IPython Notebooks in this folder are:

  1. sequencing_data_analysis.ipynb — Analysis of high-throughput sequencing data from ribosome profiling and RNA-Seq
  2. simulation.ipynbE. coli whole-cell translation simulation
  3. simulation_data_analysis.ipynb — Analysis of simulation results. Simulation results can be downloaded from Data Dryad
  4. 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

Note

  • 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.