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