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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DrugVsDisease")
In most cases, you don't need to download the package archive at all.
DrugVsDisease
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This package is for version 3.0 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: 3.0
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>
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")
| R Script | DrugVsDisease | |
| Reference Manual |
Details
| biocViews | Clustering, GeneExpression, Microarray, Software |
| Version | 2.6.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 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 |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DrugVsDisease_2.6.0.tar.gz |
| Windows Binary | DrugVsDisease_2.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DrugVsDisease_2.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | DrugVsDisease_2.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DrugVsDisease/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/DrugVsDisease/ |
| Package Downloads Report | Download Stats |
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