DrugVsDisease

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Bioconductor version: Development (3.0)

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.

Author: C. Pacini

Maintainer: j. Saez-Rodriguez <saezrodriguez at ebi.ac.uk>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("DrugVsDisease")

Citation (from within R, enter citation("DrugVsDisease")):

Documentation

PDF R Script DrugVsDisease
PDF   Reference Manual

Details

biocViews Clustering, GeneExpression, Microarray, Software
Version 2.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-3
Depends R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue
Imports annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, BiocGenerics, xtable
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Package Downloads

Package Source DrugVsDisease_2.5.0.tar.gz
Windows Binary DrugVsDisease_2.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DrugVsDisease_2.5.0.tgz
Mac OS X 10.9 (Mavericks) DrugVsDisease_2.5.0.tgz
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