DrugVsDisease
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Bioconductor version: Release (3.17)
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("DrugVsDisease")):
Installation
To install this package, start R (version "4.3") 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")| DrugVsDisease | R Script | |
| Reference Manual |
Details
| biocViews | Clustering, GeneExpression, Microarray, Software |
| Version | 2.42.0 |
| 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_2.42.0.tar.gz |
| Windows Binary | DrugVsDisease_2.42.0.zip |
| macOS Binary (x86_64) | DrugVsDisease_2.42.0.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/ |
| Package Downloads Report | Download Stats |