DrugVsDisease

DOI: 10.18129/B9.bioc.DrugVsDisease    

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Bioconductor version: Release (3.6)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DrugVsDisease")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DrugVsDisease")

 

PDF R Script DrugVsDisease
PDF   Reference Manual

Details

biocViews Clustering, GeneExpression, Microarray, Software
Version 2.20.1
In Bioconductor since BioC 2.12 (R-3.0) (5 years)
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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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DrugVsDisease_2.20.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) DrugVsDisease_2.20.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DrugVsDisease
Package Short Url http://bioconductor.org/packages/DrugVsDisease/
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Old Source Packages for BioC 3.6 Source Archive

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