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

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.

AuthorC. Pacini
Date of publicationNone
Maintainerj. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
LicenseGPL-3
Version2.14.0

View on Bioconductor

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.