GRcalculator: an online tool for calculating and mining drug response data
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)
Website design and online tool development
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:
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
# 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.