Code for Single-cell microfluidic analysis unravels individual cellular fates during Double-Strand Break Repair

Using this repository

code

This is where all the code to reproduce the Bayesian inference and simulations is contained. To reproduce the results, only files from this folder need to be run.

• data_processing The data_processing scripts will convert the output from the Matlab scripts into a cvs file which are used throughout the analysis. Running this notebook is unnecessary unless you have manipulated or generated new raw data.

• analysis The various functions used to perform inference and run stochastic simulations are contained here. In particular:

  • functions.jl contained some useful Julia functions used throughout the analysis. You should not need to work with this file directly.
  • inference_pipeline.ipynb runs the Bayesian inference on molecular data and reproduces the posterior predictions
  • inference_test.ipynb tests the Bayesian inference on synthetic data
  • variability.ipynb generates the stochastic simulations which are compared to the histogram from microfluidic all_experiments

experimental_data

The experimental data is contained in this folder

figures

All figures produced by the analysis pipeline are saved here.

LICENSE

Copyright (c) 2018 The Python Packaging Authority

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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copies of the Software, and to permit persons to whom the Software is
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The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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SOFTWARE.