DrugVsDisease: Comparison of disease and drug profiles using Gene set Enrichment Analysis

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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
Date of publication
None
Maintainer
j. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
License
GPL-3
Version
2.14.0

View on Bioconductor

Man pages

classifyprofile
Classify Profiles
combineProfiles
Combine Profiles
DrugVsDisease-package
DrugVsDisease Package Overview
generateprofiles
Generate Profiles
profiles
Gene Expression Profiles
selectrankedlists
Select Ranked Lists
selprofile
List: Differential gene expression and p-values

Files in this package

DrugVsDisease/DESCRIPTION
DrugVsDisease/NAMESPACE
DrugVsDisease/R
DrugVsDisease/R/DrugVsDisease-internal.R
DrugVsDisease/R/classifyprofile.R
DrugVsDisease/R/combineProfiles.R
DrugVsDisease/R/generateprofiles.R
DrugVsDisease/R/selectrankedlists.R
DrugVsDisease/build
DrugVsDisease/build/vignette.rds
DrugVsDisease/data
DrugVsDisease/data/customClust.rda
DrugVsDisease/data/customDB.rda
DrugVsDisease/data/customedge.rda
DrugVsDisease/data/customsif.rda
DrugVsDisease/data/datalist
DrugVsDisease/data/profiles.rda
DrugVsDisease/data/selprofile.rda
DrugVsDisease/inst
DrugVsDisease/inst/doc
DrugVsDisease/inst/doc/DrugVsDisease.R
DrugVsDisease/inst/doc/DrugVsDisease.Rnw
DrugVsDisease/inst/doc/DrugVsDisease.pdf
DrugVsDisease/inst/unitTests
DrugVsDisease/inst/unitTests/test_.KS.drug.disease.R
DrugVsDisease/inst/unitTests/test_.getESscores.R
DrugVsDisease/man
DrugVsDisease/man/DrugVsDisease-package.Rd
DrugVsDisease/man/classifyprofile.Rd
DrugVsDisease/man/combineProfiles.Rd
DrugVsDisease/man/customClust.rd
DrugVsDisease/man/customdb.rd
DrugVsDisease/man/customedge.rd
DrugVsDisease/man/customsif.rd
DrugVsDisease/man/generateprofiles.Rd
DrugVsDisease/man/profiles.Rd
DrugVsDisease/man/selectrankedlists.Rd
DrugVsDisease/man/selprofile.Rd
DrugVsDisease/tests
DrugVsDisease/tests/runTests.R
DrugVsDisease/vignettes
DrugVsDisease/vignettes/DrugVsDisease.Rnw