Code for Reproducing Analyses and Figures
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.