GSEABase: Gene set enrichment data structures and methods

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

AuthorMartin Morgan, Seth Falcon, Robert Gentleman
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.36.0

View on Bioconductor

Functions

AnnoOrEntrezIdentifier Man page
annotation<-,GeneIdentifierType,character-method Man page
annotation,GeneIdentifierType-method Man page
AnnotationIdentifier Man page
AnnotationIdentifier-class Man page
|,ANY,GeneSetCollection-method Man page
&,ANY,GeneSetCollection-method Man page
asBroadUri Man page
bcCategory Man page
bcCategory,BroadCollection-method Man page
bcSubCategory Man page
bcSubCategory,BroadCollection-method Man page
BroadCollection Man page
BroadCollection-class Man page
ChrCollection Man page
ChrCollection-class Man page
ChrlocCollection Man page
ChrlocCollection-class Man page
coerce,graphNEL,OBOCollection-method Man page
coerce,OBOCollection,graphNEL-method Man page
CollectionIdType-class Man page
|,CollectionIdType,CollectionIdType-method Man page
&,CollectionIdType,CollectionIdType-method Man page
[,CollectionIdType,missing,missing-method Man page
collectionType Man page
collectionType<- Man page
CollectionType Man page
CollectionType-class Man page
collectionType,CollectionType-method Man page
|,CollectionType,CollectionType-method Man page
&,CollectionType,CollectionType-method Man page
collectionType<-,GeneSet,CollectionType-method Man page
collectionType,GeneSet-method Man page
coloring Man page
coloring<- Man page
coloring<-,GeneColorSet,data.frame-method Man page
coloring,GeneColorSet-method Man page
ComputedCollection Man page
ComputedCollection-class Man page
contributor Man page
contributor<- Man page
contributor<-,GeneSet,character-method Man page
contributor,GeneSet-method Man page
creationDate Man page
creationDate<- Man page
creationDate<-,GeneSet,character-method Man page
creationDate,GeneSet-method Man page
description<-,GeneSet,character-method Man page
description,GeneSet-method Man page
details Man page
details,GeneColorSet-method Man page
details,GeneSet-method Man page
details-methods Man page
ENSEMBLIdentifier Man page
ENSEMBLIdentifier-class Man page
EntrezIdentifier Man page
EntrezIdentifier-class Man page
EnzymeIdentifier Man page
EnzymeIdentifier-class Man page
evidenceCode Man page
evidenceCode,GOCollection-method Man page
ExpressionSetCollection Man page
ExpressionSetCollection-class Man page
[,ExpressionSet,GeneSet,ANY-method Man page
geneColor Man page
geneColor<- Man page
geneColor<-,GeneColorSet,factor-method Man page
geneColor,GeneColorSet-method Man page
GeneColorSet Man page
GeneColorSet,BroadCollection-method Man page
[,GeneColorSet,character,ANY-method Man page
|,GeneColorSet,character-method Man page
[[,GeneColorSet,character-method Man page
&,GeneColorSet,character-method Man page
GeneColorSet,character-method Man page
GeneColorSet-class Man page
GeneColorSet,ExpressionSet-method Man page
|,GeneColorSet,GeneColorSet-method Man page
&,GeneColorSet,GeneColorSet-method Man page
GeneColorSet,GeneIdentifierType-method Man page
GeneColorSet,GeneSet-method Man page
GeneColorSet,GOCollection-method Man page
$,GeneColorSet-method Man page
GeneColorSet-methods Man page
GeneColorSet,missing-method Man page
[,GeneColorSet,numeric,ANY-method Man page
[[,GeneColorSet,numeric-method Man page
GeneIdentifierType Man page
GeneIdentifierType-class Man page
geneIds Man page
geneIds<- Man page
geneIds<-,GeneSet,character-method Man page
geneIds<-,GeneSetCollection,list-method Man page
geneIds,GeneSetCollection-method Man page
geneIds,GeneSet-method Man page
geneIdType Man page
geneIdType<- Man page
geneIdType,GeneIdentifierType-method Man page
geneIdType<-,GeneSet,character-method Man page
geneIdType<-,GeneSet,GeneIdentifierType-method Man page
geneIdType,GeneSet-method Man page
GenenameIdentifier Man page
GenenameIdentifier-class Man page
GeneSet Man page
GeneSet,BroadCollection-method Man page
[,GeneSet,character,ANY-method Man page
|,GeneSet,character-method Man page
[[,GeneSet,character-method Man page
&,GeneSet,character-method Man page
GeneSet,character-method Man page
GeneSet-class Man page
GeneSetCollection Man page
[<-,GeneSetCollection,ANY,ANY,ANY-method Man page
[[<-,GeneSetCollection,ANY,ANY,ANY-method Man page
[<-,GeneSetCollection,ANY,ANY,GeneSet-method Man page
|,GeneSetCollection,ANY-method Man page
&,GeneSetCollection,ANY-method Man page
GeneSetCollection,character,AnnotationIdentifier,ChrlocCollectio Man page
GeneSetCollection,character,AnnotationIdentifier,CollectionIdTyp Man page
GeneSetCollection,character,AnnotationIdentifier,CollectionType- Man page
GeneSetCollection,character,AnnotationIdentifier,GOCollection-me Man page
GeneSetCollection,character,AnnotationIdentifier,PfamCollection- Man page
GeneSetCollection,character,AnnotationIdentifier,PrositeCollecti Man page
[<-,GeneSetCollection,character,ANY,GeneSet-method Man page
[[<-,GeneSetCollection,character,ANY,GeneSet-method Man page
[,GeneSetCollection,character,ANY-method Man page
[[,GeneSetCollection,character-method Man page
GeneSetCollection-class Man page
GeneSetCollection,ExpressionSet,missing,ChrlocCollection-method Man page
GeneSetCollection,ExpressionSet,missing,CollectionIdType-method Man page
GeneSetCollection,ExpressionSet,missing,CollectionType-method Man page
GeneSetCollection,ExpressionSet,missing,GOCollection-method Man page
GeneSetCollection,ExpressionSet,missing,KEGGCollection-method Man page
GeneSetCollection,ExpressionSet,missing,PfamCollection-method Man page
GeneSetCollection,ExpressionSet,missing,PrositeCollection-method Man page
|,GeneSetCollection,GeneSetCollection-method Man page
&,GeneSetCollection,GeneSetCollection-method Man page
GeneSetCollection,GeneSet,missing,missing-method Man page
GeneSetCollection,GOAllFrame,missing,GOCollection-method Man page
GeneSetCollection,KEGGFrame,missing,KEGGCollection-method Man page
GeneSetCollection,list,missing,missing-method Man page
[,GeneSetCollection,logical,ANY-method Man page
GeneSetCollection-methods Man page
GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType- Man page
GeneSetCollection,missing,AnnotationIdentifier,CollectionType-me Man page
GeneSetCollection,missing,AnnotationIdentifier,GOCollection-meth Man page
GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-me Man page
[[<-,GeneSetCollection,numeric,ANY,GeneSet-method Man page
[,GeneSetCollection,numeric,ANY-method Man page
GeneSet,ExpressionSet-method Man page
GeneSet,GeneIdentifierType-method Man page
|,GeneSet,GeneSet-method Man page
&,GeneSet,GeneSet-method Man page
GeneSet,GOCollection-method Man page
$,GeneSet-method Man page
GeneSet-methods Man page
GeneSet,missing-method Man page
[,GeneSet,numeric,ANY-method Man page
[[,GeneSet,numeric-method Man page
getBroadSets Man page
getGmt Man page
getOBOCollection Man page
GOAllFrameIdentifier Man page
GOAllFrameIdentifier-class Man page
GOCollection Man page
GOCollection-class Man page
[,GOCollection,missing,missing-method Man page
goIds Man page
goIds,GOCollection-method Man page
goSlim Man page
goSlim,ExpressionSet,GOCollection-method Man page
goSlim,GOCollection,GOCollection-method Man page
goSlim-methods Man page
GSEABase Man page
GSEABase-package Man page
ids Man page
ids,CollectionIdType-method Man page
incidence Man page
incidence,GeneSetCollection-method Man page
incidence,GeneSet-method Man page
incidence-methods Man page
initialize,GeneColorSet-method Man page
initialize,GeneIdentifierType-method Man page
initialize,GeneSet-method Man page
intersect,ANY,GeneSetCollection-method Man page
intersect,CollectionIdType,CollectionIdType-method Man page
intersect,CollectionType,CollectionType-method Man page
intersect,GeneColorSet,GeneColorSet-method Man page
intersect,GeneSetCollection,ANY-method Man page
intersect,GeneSet,GeneSet-method Man page
io Man page
KEGGCollection Man page
KEGGCollection-class Man page
KEGGFrameIdentifier Man page
KEGGFrameIdentifier-class Man page
Logic,character,GeneSetCollection-method Man page
Logic,character,GeneSet-method Man page
Logic,CollectionIdType,CollectionIdType-method Man page
Logic,CollectionType,CollectionType-method Man page
Logic,GeneSet,GeneSetCollection-method Man page
longDescription Man page
longDescription<- Man page
longDescription<-,GeneSet,character-method Man page
longDescription,GeneSet-method Man page
MapCollection Man page
MapCollection-class Man page
mapIdentifiers Man page
mapIdentifiers,ANY,ANY,ANY-method Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-metho Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierTyp Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-me Man page
mapIdentifiers,GeneColorSet,NullIdentifier,GeneIdentifierType-me Man page
mapIdentifiers,GeneSetCollection,GeneIdentifierType,missing-meth Man page
mapIdentifiers,GeneSet,GeneIdentifierType,AnnDbBimap-method Man page
mapIdentifiers,GeneSet,GeneIdentifierType,environment-method Man page
mapIdentifiers,GeneSet,GeneIdentifierType,GeneIdentifierType-met Man page
mapIdentifiers,GeneSet,GeneIdentifierType,missing-method Man page
mapIdentifiers,GeneSet,GeneIdentifierType,NullIdentifier-method Man page
mapIdentifiers,GeneSet,NullIdentifier,GeneIdentifierType-method Man page
mapIdentifiers-methods Man page
names,GeneSetCollection-method Man page
NullCollection Man page
NullCollection-class Man page
NullIdentifier Man page
NullIdentifier-class Man page
OBOCollection Man page
[,OBOCollection,character,missing-method Man page
OBOCollection-class Man page
OMIMCollection Man page
OMIMCollection-class Man page
ontology Man page
ontology,GOCollection-method Man page
organism Man page
organism<- Man page
organism,GeneIdentifierType-method Man page
organism<-,GeneSet,character-method Man page
organism,GeneSet-method Man page
organism,GOAllFrameIdentifier-method Man page
organism,KEGGFrameIdentifier-method Man page
PfamCollection Man page
PfamCollection-class Man page
phenotype Man page
phenotype<- Man page
phenotypeColor Man page
phenotypeColor<- Man page
phenotypeColor<-,GeneColorSet,factor-method Man page
phenotypeColor,GeneColorSet-method Man page
phenotype<-,GeneColorSet,character-method Man page
phenotype,GeneColorSet-method Man page
PMIDCollection Man page
PMIDCollection-class Man page
PrositeCollection Man page
PrositeCollection-class Man page
pubMedIds<-,GeneSet,character-method Man page
pubMedIds,GeneSet-method Man page
RefseqIdentifier Man page
RefseqIdentifier-class Man page
setdiff,ANY,GeneSetCollection-method Man page
setdiff,CollectionIdType,CollectionIdType-method Man page
setdiff,CollectionType,CollectionType-method Man page
setdiff,GeneColorSet,GeneColorSet-method Man page
setdiff,GeneSetCollection,ANY-method Man page
setdiff,GeneSet,GeneSet-method Man page
setIdentifier Man page
setIdentifier<- Man page
setIdentifier<-,GeneSet,character-method Man page
setIdentifier,GeneSet-method Man page
setName Man page
setName<- Man page
setName<-,GeneSet,character-method Man page
setName,GeneSet-method Man page
setVersion Man page
setVersion<- Man page
setVersion,GeneSet-method Man page
setVersion<-,GeneSet,Versions-method Man page
show,AnnotationIdentifier-method Man page
show,BroadCollection-method Man page
show,CollectionIdType-method Man page
show,CollectionType-method Man page
show,GeneColorSet-method Man page
show,GeneIdentifierType-method Man page
show,GeneSetCollection-method Man page
show,GeneSet-method Man page
show,GOCollection-method Man page
show,OBOCollection-method Man page
subsets Man page
subsets,OBOCollection-method Man page
SymbolIdentifier Man page
SymbolIdentifier-class Man page
toBroadXML Man page
toGmt Man page
toGmt,GeneSetCollection-method Man page
toGmt,GeneSet-method Man page
UnigeneIdentifier Man page
UnigeneIdentifier-class Man page
union,ANY,GeneSetCollection-method Man page
union,CollectionIdType,CollectionIdType-method Man page
union,CollectionType,CollectionType-method Man page
union,GeneColorSet,GeneColorSet-method Man page
union,GeneSetCollection,ANY-method Man page
union,GeneSet,GeneSet-method Man page
UniprotIdentifier Man page
UniprotIdentifier-class Man page
updateObject,GeneSetCollection-method Man page
urls Man page
urls<- Man page
urls<-,GeneSet,character-method Man page
urls,GeneSet-method Man page

Files

GSEABase/DESCRIPTION
GSEABase/NAMESPACE
GSEABase/NEWS
GSEABase/R
GSEABase/R/AAA.R GSEABase/R/AllClasses.R GSEABase/R/AllGenerics.R GSEABase/R/getObjects.R GSEABase/R/methods-CollectionType.R GSEABase/R/methods-ExpressionSet.R GSEABase/R/methods-GeneColorSet.R GSEABase/R/methods-GeneIdentifierType.R GSEABase/R/methods-GeneSet.R GSEABase/R/methods-GeneSetCollection.R GSEABase/R/methods-OBOCollection.R GSEABase/R/utilities.R
GSEABase/build
GSEABase/build/vignette.rds
GSEABase/inst
GSEABase/inst/doc
GSEABase/inst/doc/GSEABase.R
GSEABase/inst/doc/GSEABase.Rnw
GSEABase/inst/doc/GSEABase.pdf
GSEABase/inst/extdata
GSEABase/inst/extdata/Broad.xml
GSEABase/inst/extdata/Broad1.xml
GSEABase/inst/extdata/goslim_plant.obo
GSEABase/inst/unitTests
GSEABase/inst/unitTests/test_CollectionType.R
GSEABase/inst/unitTests/test_ExpressionSet.R
GSEABase/inst/unitTests/test_GeneColorSet.R
GSEABase/inst/unitTests/test_GeneIdentifierType.R
GSEABase/inst/unitTests/test_GeneSet.R
GSEABase/inst/unitTests/test_GeneSetCollection.R
GSEABase/inst/unitTests/test_OBOCollection.R
GSEABase/inst/unitTests/test_getGeneSets.R
GSEABase/inst/unitTests/test_utilities.R
GSEABase/man
GSEABase/man/CollectionType-class.Rd GSEABase/man/CollectionType-constructors.Rd GSEABase/man/GSEABase-package.Rd GSEABase/man/GeneColorSet-class.Rd GSEABase/man/GeneColorSet-methods.Rd GSEABase/man/GeneIdentifierType-class.Rd GSEABase/man/GeneIdentifierType-constructors.Rd GSEABase/man/GeneSet-class.Rd GSEABase/man/GeneSet-methods.Rd GSEABase/man/GeneSetCollection-class.Rd GSEABase/man/GeneSetCollection-methods.Rd GSEABase/man/OBOCollection-class.Rd GSEABase/man/details-methods.Rd GSEABase/man/getOBOCollection.Rd GSEABase/man/getObjects.Rd GSEABase/man/goSlim-methods.Rd GSEABase/man/incidence-methods.Rd GSEABase/man/mapIdentifiers-methods.Rd
GSEABase/tests
GSEABase/tests/unitTests.R
GSEABase/vignettes
GSEABase/vignettes/GSEABase.Rnw

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