DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles
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README.md

README.md

Drug vs. Disease

Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Dynamic access to both Array Express and GEO is provided, with automatic annotation and generation of differential expression profiles. These profiles can be compared to a reference set of profiles from the Connectivity Map or to a users own set of data. Correlations between profiles are calculated using Gene Set Enrichment Analysis. Resulting matches between drug and disease profiles can be viewed in a network representation within the Cytoscape plug-in. Negatively correlated (enriched) profiles can be used to generate hypotheses of drug-repurposing whilst positively correlated (enriched) profiles may be used to infer side-effects of drugs.

Available from Bioconductor: Bioconductor/DvDdata

Citation:

Pacini, C., Iorio, F., Gonçalves, E., Iskar, M., Klabunde, T., Bork, P., Saez-Rodriguez, J. DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics (Oxford, England). Nov 4, Volume 29, Number 1, (2013), p.132-134 https://doi.org/10.1093/bioinformatics/bts656

Installation instructions for R packages

  1. Make sure you have R installed. You can download it from http://cran.ma.imperial.ac.uk/.

Note: We recommend use the 2.15 version of R

  1. For Mac users you will need to have installed the tcltk add-on for R. This can be downloaded from http://cran.r-project.org/bin/macosx/tools/tcltk-8.5.5-x11.dmg.

  2. Open R console.

  3. First install the dependencies which are required for the DvD package. Download the R script DvDdependencies.R, this script will automatically check for and if necessary install R packages required by DvD.

source("~/DvDdependencies.R") #where "~/" should be the directory where the source file is stored
  1. To install the DrugVsDiseasedata package. Download the source file DrugVsDiseasedata_0.99.2.tar.gz
install.packages("~/DrugVsDiseasedata_0.99.2.tar.gz",type="source") #note "~/" should point to the directory where the file is saved
library(DrugVsDiseasedata)
  1. To install the cMap2data package. Downloadthe source file cMap2data_0.99.1.tar.gz
install.packages("~/cMap2data_0.99.1.tar.gz",type="source") #note "~/" should point to the directory where the file is saved
library(cMap2data) 
  1. Finally download and install the DrugVsDisease package (DrugVsDisease_1.1.2.tar.gz)
install.packages("~/DrugVsDisease_1.1.2.tar.gz",type="source") #note "~/" should point to the directory where the file is saved
library(DrugVsDisease)

Installation instructions for Cytoscape plug-in

  1. Make sure you have installed DvD, DvDdata and dependencies as above. Install Rserve. It is a R package that enables communication between Java and R. Enter the following commands in R console:
    install.packages("Rserve") # This command only needs to be typed once
    library(Rserve)
    Rserve(args="--vanilla")

Note: Rserve is only disabled if you restart your pc. Thus, if you want to use Rserve after reboot you have to call it again.
On Windows Rserve may also stop working if an error is encountered.

  1. Make sure you have Cytoscape installed. You can download it from http://www.cytoscape.org/download.html.

Note: We recommend use the 2.8.3 version of Cytoscape

  1. Install DvD plugin.
    1. Download DvD plug-in jar file here.
    2. In Cytoscape go to 'Plugins' -> 'Install Plugin from File'
    3. Search for DvD jar file.
    4. DvD is now installed.

IMPORTANT: Before using DvD on Ubuntu you need to type on Terminal

sudo apt-get install libcairo2-dev 	
sudo apt-get install libxt-dev