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DrugVsDisease

This is the development version of DrugVsDisease; for the stable release version, see DrugVsDisease.

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
DrugVsDisease PDF R Script
Reference Manual PDF

Details

biocViews Clustering, GeneExpression, Microarray, Software
Version 2.43.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 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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Package Archives

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

Source Package DrugVsDisease_2.43.0.tar.gz
Windows Binary DrugVsDisease_2.43.0.zip
macOS Binary (x86_64) DrugVsDisease_2.43.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DrugVsDisease
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DrugVsDisease
Bioc Package Browser https://code.bioconductor.org/browse/DrugVsDisease/
Package Short Url https://bioconductor.org/packages/DrugVsDisease/
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