DrugVsDisease: Comparison of disease and drug profiles using Gene set Enrichment Analysis
Version 2.16.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorC. Pacini
Bioconductor views Clustering GeneExpression Microarray
Date of publicationNone
Maintainerj. Saez-Rodriguez <saezrodriguez@ebi.ac.uk>
LicenseGPL-3
Version2.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DrugVsDisease")

Man pages

classifyprofile: Classify Profiles
combineProfiles: Combine Profiles
customClust: Custom Clusters
customdb: Custom Gene Expression Profiles
customedge: Edge attributes for example custom network
customsif: SIF file for custom clusters
DrugVsDisease-package: DrugVsDisease Package Overview
generateprofiles: Generate Profiles
profiles: Gene Expression Profiles
selectrankedlists: Select Ranked Lists
selprofile: List: Differential gene expression and p-values

Functions

DrugVsDisease Man page
DrugVsDisease-package Man page
KS.drug.disease Source code
WSR Source code
averagecluster Source code
calculateES Source code
classifyaveragelinkage Source code
classifyprofile Man page Source code
classifysinglelinkage Source code
combineEnsembl Source code
combineProfiles Man page Source code
combined Source code
combinemed Source code
convertEnsembl Source code
convertProbes Source code
customClust Man page
customDB Man page
customedge Man page
customsif Man page
datafromAE Source code
datafromGEO Source code
findCluster Source code
findSignifCompounds Source code
fitlms Source code
generateprofiles Man page Source code
getESscores Source code
matrixVar Source code
maxvar Source code
mrs Source code
multcontrast Source code
norm_mrs Source code
normalisedata Source code
processplatforms Source code
profiles Man page
ptog Source code
ranknamemat Source code
readlocalAE Source code
readlocalCEL Source code
selectrankedlists Man page Source code
selprofile Man page
significantES Source code
singlecontrast Source code
treatmentonlyfit Source code
writecytoscape Source code

Files

DESCRIPTION
NAMESPACE
R
R/DrugVsDisease-internal.R
R/classifyprofile.R
R/combineProfiles.R
R/generateprofiles.R
R/selectrankedlists.R
build
build/vignette.rds
data
data/customClust.rda
data/customDB.rda
data/customedge.rda
data/customsif.rda
data/datalist
data/profiles.rda
data/selprofile.rda
inst
inst/doc
inst/doc/DrugVsDisease.R
inst/doc/DrugVsDisease.Rnw
inst/doc/DrugVsDisease.pdf
inst/unitTests
inst/unitTests/test_.KS.drug.disease.R
inst/unitTests/test_.getESscores.R
man
man/DrugVsDisease-package.Rd
man/classifyprofile.Rd
man/combineProfiles.Rd
man/customClust.rd
man/customdb.rd
man/customedge.rd
man/customsif.rd
man/generateprofiles.Rd
man/profiles.Rd
man/selectrankedlists.Rd
man/selprofile.Rd
tests
tests/runTests.R
vignettes
vignettes/DrugVsDisease.Rnw
DrugVsDisease documentation built on May 20, 2017, 10:52 p.m.