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Comparative network reconstruction analyses

This repository contains the code used to perform the analyses in our publication: "Comparative Network Reconstruction using Mixed Integer Programming", Bosdriesz et al., Bioinformatics (2018) https://doi.org/10.1093/bioinformatics/bty616

The code for the CNR method has it's own repository: https://github.com/NKI-CCB/cnr

Contents of this repository:

  • /orton: contains code to simulate and reconstruct the orton model. This corresponds to Fig 2 and Fig S2-S5. It contains the following files:

    • ortonModelExtended.pkl - pickle object with orton model description
    • odemod.py - python module to perform orton model simulations
    • Model-simulations.ipyn - Notebook in which the simulations are performed
    • Model-calculate-true-rloc.ipyn - Notebook to estimate the true local response coefficients directly from the orton model.
    • CNR-plot-roc.R - Fig 2B and S2. Requires first running scripts/CNR-scan-noise.py and scripts/extract-roc-data.py
    • CNR-scan-theta.ipyn - Fig 2C
    • CNR-plot-reconstruction.ipyn - Fig 2D and S3
    • CNR-plot-npert.R Fig 2EF, S4 and S5. Requires first running scripts/CNR-npert-correlation.py, scripts/CNR-npert-correlation-priornetwork.py and CNR-analyze-npert-correlation.ipynb

  • /ptpn11ko-persisters: contains the perturbation data and the network reconstruction of the VACO, VACO PTPN11 KO, and VACO persister cells. This corresponds to Fig 3C and 4.