synergy 0.1.0

Python package for calculating drug combination synergy

synergy

A python package to calculate, analyze, and visualize drug combination synergy and antagonism. Currently supports multiple models of synergy, including MuSyC, Bliss, Loewe, Combination Index, ZIP, Zimmer, Schindler, and HSA.

Installation

Using PIP pip install synergy

Using conda not yet

Using git git clone ...

Requirements

• python >= 3.5
• numpy >= 1.13.0
• scipy >= 0.18.0
• Optional for full plotting functionality
  • matplotlib
  • plotly

Current features

• Calculate two-drug synergy using
  • Parametric
    • MuSyC
    • Zimmer (effective dose model)
    • BRAID
  • Dose-dependent
    • Bliss
    • Loewe
    • Schindler
    • ZIP
    • HSA
    • Combination Index
• Residual bootstrap re-sampling to obtain confidence intervals for parameters of parametric models
• Single drug models
  • Parametric
    • Four-parameter Hill equation
    • Two-parameter Hill equation
    • Median-effect equation
  • Non-parametric
    • Piecewise linear
• Model scoring
  • R-squared
  • Akaike Information Criterion
  • Bayesian Information Criterion
• Visualization
  • Heatmaps
  • 3D Plotly Surfaces
• Synthetic data tools
  • Drug dilutions using grid-based sampling
  • "Sham experiment" simulation

Planned features

• Additional models
  • Parametric
    • GPDI
• Three+ drug combinations (when possible)
  • MuSyC
  • Bliss
  • Loewe / CI
  • HSA
  • Schindler
  • Zimmer (at least incorporating pairwise synergies)
• Visualization
  • Highlight single-drug curves on 3D surface plots
  • matplotlib 3D surface plotting
  • Contour plots for heatmaps
  • Isobolgrams
• Additional dose / experiment design tools
  • Alternative dosing strategies
• Heteroskedastic re-sampling for datasets with >= 3 replicates at each dose
• Parallelization API for fitting high-throughput screen data

License

GNU General Public License v3 or later (GPLv3+)