nki-ccb/cnr-analyses

Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., Bioinformatics, 2018)

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.