GRcalculator is a Shiny application (http://www.grcalculator.org) developed to accompany the Nature paper Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs by Hafner et al. (2016).

For a brief overview of the GRcalculator and the importance of the newly developed GR metrics methodology (Hafner et al. 2016), see this poster: https://figshare.com/articles/GRcalculator_an_online_tool_for_calculating_and_mining_drug_response_data/4244408

Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, et al. GRcalculator: an online tool for calculating and mining dose–response data. BMC Cancer 2017, 17(1):698. (https://doi.org/10.1186/s12885-017-3689-3)

Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nature Methods 2016, 13(6):521-527. (https://doi.org/10.1038/nmeth.3853)

Nick Clark¹, Marc Hafner², Michal Kouril¹, Mario Niepel², Elizabeth Williams², Jeremy Muhlich² and Mario Medvedovic¹

¹ LINCS-BD2K Data Coordination and Integration Center, University of Cincinnati

² HMS LINCS Center, Harvard Medical School

Install R package dependencies:

# Install our "GRmetrics" Bioconductor package and others
source("http://bioconductor.org/biocLite.R")
biocLite("GRmetrics")
biocLite("S4Vectors")
# Install our "shinyLi" package
install.packages("devtools")
devtools::install_github("uc-bd2k/shinyLi")
# Install CRAN package dependencies
install.packages(c("shiny","shinyjs","shinyBS","ggplot2","plotly","drc","stringr","readr", "formattable", "plyr", "markdown"))

Run the application from the R command line:

shiny::runGitHub('uc-bd2k/grcalculator')

The GRcalculator tool (http://www.grcalculator.org) is implemented in the form of three integrated Shiny applications (grcalculator, grbrowser and grtutorial).

The grtutorial Shiny application (“About GR Metrics” link in the toolbar) provides background information about the advantages of the GR metrics over traditional metrics for quantifying dose-response assays as well as descriptions of the GRcalculator tools.

The grbrowser Shiny application (“LINCS Dose-Response Datasets” section in the toolbar) facilitates interactive browsing and mining of drug response data generated by the LINCS project.

This package re-creates the online calculation and visualization tools available at http://www.grcalculator.org/grcalculator/.

Bioconductor page: https://bioconductor.org/packages/GRmetrics

Vignette: https://bioconductor.org/packages/release/bioc/vignettes/GRmetrics/inst/doc/GRmetrics-vignette.html

# Use the following code to install the GRmetrics package in R
source("http://bioconductor.org/biocLite.R")
biocLite("GRmetrics")

This repository contains the MATLAB, Python, and R implementations of GR metrics calculations with examples and supplementary information.