DrugVsDisease

DOI: 10.18129/B9.bioc.DrugVsDisease    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DrugVsDisease.

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DrugVsDisease")

For older versions of R, please refer to the appropriate Bioconductor release.

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	2.24.2
In Bioconductor since	BioC 2.12 (R-3.0) (6 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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Package Archives

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

Source Package	DrugVsDisease_2.24.2.tar.gz
Windows Binary	DrugVsDisease_2.24.2.zip
Mac OS X 10.11 (El Capitan)	DrugVsDisease_2.24.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DrugVsDisease
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DrugVsDisease
Package Short Url	http://bioconductor.org/packages/DrugVsDisease/
Package Downloads Report	Download Stats