.GeneSetDb	GeneSetDb-class
.SparrowResult	SparrowResult
addCollectionMetadata	collectionMetadata
addGeneSetMetadata	addGeneSetMetadata
all.equal.GeneSetDb	all.equal.GeneSetDb
annotateGeneSetMembership	annotateGeneSetMembership
as.data.frame	conversion
as.data.frame.GeneSetDb	conversion
as.data.table	conversion
as.data.table.GeneSetDb	conversion
as.list	conversion
calculateIndividualLogFC	calculateIndividualLogFC
collectionMetadata	collectionMetadata
collectionMetadata,GeneSetDb,character,character-method	collectionMetadata
collectionMetadata,GeneSetDb,character,missing-method	collectionMetadata
collectionMetadata,GeneSetDb,missing,missing-method	collectionMetadata
combine,GeneSetDb,GeneSetDb-method	combine-GeneSetDb-GeneSetDb-method
combine,SparrowResult,SparrowResult-method	combine-SparrowResult-SparrowResult-method
conform	conform
conform,GeneSetDb-method	conform
conversion	conversion
convertIdentifiers	convertIdentifiers
convertIdentifiers,BiocSet-method	convertIdentifiers
convertIdentifiers,GeneSetDb-method	convertIdentifiers
corplot	corplot
eigenWeightedMean	eigenWeightedMean
encode_gskey	gskey
exampleBiocSet	examples
exampleDgeResult	examples
exampleExpressionSet	examples
exampleGeneSetDb	examples
exampleGeneSetDF	examples
exampleGeneSets	examples
exampleSparrowResult	examples
failWith	failWith
featureIdMap	featureIdMap
featureIdMap,GeneSetDb-method	featureIdMap
featureIds	featureIds
featureIds,GeneSetDb-method	featureIds
featureIds,SparrowResult-method	featureIds
featureIdType	collectionMetadata
featureIdType,GeneSetDb-method	collectionMetadata
featureIdType<-	collectionMetadata
featureIdType<-,GeneSetDb-method	collectionMetadata
geneSet	geneSet
geneSet,GeneSetDb-method	geneSet
geneSet,SparrowResult-method	geneSet
geneSetCollectionURLfunction	geneSetCollectionURLfunction
geneSetCollectionURLfunction,GeneSetDb-method	geneSetCollectionURLfunction
geneSetCollectionURLfunction,SparrowResult-method	geneSetCollectionURLfunction
geneSetCollectionURLfunction<-	geneSetCollectionURLfunction
geneSetCollectionURLfunction<-,GeneSetDb-method	geneSetCollectionURLfunction
GeneSetDb	GeneSetDb-class
geneSetDb	SparrowResult-utilities
GeneSetDb-class	GeneSetDb-class
geneSets	geneSets
geneSets,GeneSetDb-method	geneSets
geneSets,SparrowResult-method	geneSets
geneSetsStats	geneSetsStats
geneSetSummaryByGenes	geneSetSummaryByGenes
geneSetSummaryByGenes,GeneSetDb-method	geneSetSummaryByGenes
geneSetSummaryByGenes,SparrowResult-method	geneSetSummaryByGenes
geneSetURL	collectionMetadata
geneSetURL,GeneSetDb-method	collectionMetadata
geneSetURL,SparrowResult-method	collectionMetadata
getKeggCollection	getKeggCollection
getKeggGeneSetDb	getKeggCollection
getMSigCollection	getMSigCollection
getMSigGeneSetDb	getMSigCollection
getPantherCollection	getPantherCollection
getPantherGeneSetDb	getPantherCollection
getReactomeCollection	getReactomeCollection
getReactomeGeneSetDb	getReactomeCollection
goseq	goseq
gsdScore	gsdScore
hasGeneSet	hasGeneSet
hasGeneSetCollection	hasGeneSetCollection
incidenceMatrix	incidenceMatrix
iplot	iplot
is.active	is.active
is.conformed	conform
length,GeneSetDb-method	geneSets
logFC	logFC
mgheatmap	mgheatmap
mgheatmap2	mgheatmap2
msg	msg
nrow,GeneSetDb-method	geneSets
ora	ora
p.matrix	p.matrix
plot_ora_bias	ora
randomGeneSetDb	randomGeneSetDb
renameCollections	renameCollections
renameRows	renameRows
result	results
result.SparrowResult	results
resultNames	results
results	results
scale_rows	scale_rows
scoreSingleSamples	scoreSingleSamples
seas	seas
SparrowResult	SparrowResult
SparrowResult-class	SparrowResult
sparrow_methods	sparrow_methods
species_info	species_info
split_gskey	gskey
ssGSEA.normalize	ssGSEA.normalize
subset.GeneSetDb	subset.GeneSetDb
subsetByFeatures	subsetByFeatures
subsetByFeatures,GeneSetDb-method	subsetByFeatures
tabulateResults	results
unconform	conform
unconform,GeneSetDb-method	conform
validateInputs	validateInputs
volcanoPlot	volcanoPlot
volcanoStatsTable	volcanoStatsTable
zScore	zScore
[,GeneSetDb,ANY,ANY,ANY-method	sub-GeneSetDb-ANY-ANY-ANY-method
