synergy 0.0.1

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, inclding MuSyC, Bliss, Loewe, Combination Index, ZIP, Zimmer, Schindler, and HSA.

Note, this package was not used to calculate MuSyC or others' synergy in "Quantifying Drug Combination Synergy along Potency and Efficacy Axes" (https://doi.org/10.1016/j.cels.2019.01.003), nor "A Consensus Framework Unifies Multi-Drug Synergy Metrics" (https://doi.org/10.1101/683433). It is a standalone implementation.

Installation

Using PIP not yet

Using conda not yet

Using git git clone ...

Requirements

• python 3
• numpy
• scipy
• Optional for full plotting functionality
  • matplotlib
  • plotly
  • pandas

Current features

• Calculate two-drug synergy using
  • Parametric
    • MuSyC
    • Zimmer (effective dose model)
  • Dose-dependent
    • Bliss
    • Loewe
    • Schindler
    • ZIP
    • HSA
    • Combination Index
• Single drug models
  • Four-parameter Hill equation
  • Two-parameter Hill equation
  • Median-effect equation
  • 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
    • BRAID
• Three+ drug combinations (when possible)
• 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
• Monte carlo sampling to obtain confidence intervals for parameters
• Parallelization API for fitting high-throughput screen data

Current version

0.0.1

License

GNU General Public License v3 or later (GPLv3+)