DrugVsDisease

DOI: 10.18129/B9.bioc.DrugVsDisease    

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Bioconductor version: Release (3.14)

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 (version "4.1") and enter:

if (!require("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 2.36.0
In Bioconductor since BioC 2.12 (R-3.0) (9 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
Links To Me
Build Report  

Package Archives

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

Source Package DrugVsDisease_2.36.0.tar.gz
Windows Binary DrugVsDisease_2.36.0.zip
macOS 10.13 (High Sierra) DrugVsDisease_2.36.0.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 https://bioconductor.org/packages/DrugVsDisease/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: