dose-response and synergy analysis for drug screening data
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README.md

drexplorer

The drexplorer R package is developed to facilitate the analysis of dose-response data. It can be used to:

  • assess the reproducibility of replicates,
  • detect outlier data points
  • fit different models
  • select the best model
  • estimate IC (Inhibition Concentration, e.g. IC50) values at different percentiles
  • evaluate drug-drug interactions using interaction index
  • implement NCI 60 method (estimation of GI50, TGI, LD50)
  • implement Hill equation (Estimation of EC50, Emax, Einf, E0 and Hill slope)
  • Calculate AUC (Area Under Curve) for all models

A figure summary of its functions can be found from our paper (figure cited from PubMed Central):

drexplorer examples

Installation

The devtools package is used to install R packages hosted on Github. To install drexplorer, type the following commands in the R console:

    library(devtools)
    install_github("nickytong/drexplorer")

Usage

# load the package
library(drexplorer)
	
# pull out vignette: vignette does not pull out correctly if installed on Linux with non-root (R>3.0)
# instead, check vignette at: http://htmlpreview.github.com/?https://github.com/nickytong/drexplorer/blob/master/inst/doc/drexplorer.html
vignette('drexplorer')
	
# GUI for dose-response curve fitting
drexplorerGUI_1()
	
# GUI for drug-drug interaction
drexplorerGUI_2()

User Manual

A manual is available. This is the same document as shown by typing the following command in R console.

vignette('drexplorer')

Cite Us

The drexplorer package has been published in Bioinformatics which can be cited as:

Tong, Pan, Kevin R. Coombes, Faye M. Johnson, Lauren A. Byers, Lixia Diao, Diane D. Liu, J. Jack Lee, John V. Heymach, and Jing Wang. "drexplorer: A tool to explore dose–response relationships and drug–drug interactions." Bioinformatics (2015): btv028. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426846/