Python package for calculating drug combination synergy
Project description
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
- Parametric
- 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
- Parametric
- 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+)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.