Metadata-Version: 2.1
Name: synergy
Version: 0.0.1
Summary: Python package for calculating drug combination synergy
Home-page: https://github.com/djwooten/synergy
Author: David J. Wooten
Author-email: dwooten@psu.edu
License: UNKNOWN
Description: <img src="logo.png" width="400" />
        
        # 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+)
        
Keywords: synergy drug combination pharmacology cancer
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.7
Description-Content-Type: text/markdown
