calcAgreement	calcAgreement
calcAlignment	calcAlignment
calcAlignmentPerCluster	calcAlignmentPerCluster
calcARI	calcARI
calcDatasetSpecificity	calcDatasetSpecificity
calcGeneVars	calcGeneVars
calcPurity	calcPurity
convertOldLiger	convertOldLiger
createLiger	createLiger
getFactorMarkers	getFactorMarkers
getGeneValues	getGeneValues
getProportionMito	getProportionMito
imputeKNN	imputeKNN
liger	liger-class
liger-class	liger-class
ligerToSeurat	ligerToSeurat
linkGenesAndPeaks	linkGenesAndPeaks
louvainCluster	louvainCluster
makeFeatureMatrix	makeFeatureMatrix
makeInteractTrack	makeInteractTrack
makeRiverplot	makeRiverplot
mergeH5	mergeH5
nnzeroGroups	nnzeroGroups
nnzeroGroups.dgCMatrix	nnzeroGroups
nnzeroGroups.matrix	nnzeroGroups
nonneg	nonneg
normalize	normalize
online_iNMF	online_iNMF
optimizeALS	optimizeALS
optimizeALS.liger	optimizeALS
optimizeALS.list	optimizeALS
optimizeNewData	optimizeNewData
optimizeNewK	optimizeNewK
optimizeNewLambda	optimizeNewLambda
optimizeSubset	optimizeSubset
plotByDatasetAndCluster	plotByDatasetAndCluster
plotClusterFactors	plotClusterFactors
plotClusterProportions	plotClusterProportions
plotFactors	plotFactors
plotFeature	plotFeature
plotGene	plotGene
plotGeneLoadings	plotGeneLoadings
plotGenes	plotGenes
plotGeneViolin	plotGeneViolin
plotWordClouds	plotWordClouds
quantileAlignSNF	quantileAlignSNF
quantile_norm	quantile_norm
quantile_norm.liger	quantile_norm
quantile_norm.list	quantile_norm
rank_matrix	rank_matrix
rank_matrix.dgCMatrix	rank_matrix
rank_matrix.matrix	rank_matrix
read10X	read10X
readSubset	readSubset
removeMissingObs	removeMissingObs
reorganizeLiger	reorganizeLiger
restoreOnlineLiger	restoreOnlineLiger
runGSEA	runGSEA
runTSNE	runTSNE
runUMAP	runUMAP
runWilcoxon	runWilcoxon
scaleNotCenter	scaleNotCenter
selectGenes	selectGenes
seuratToLiger	seuratToLiger
show	show-methods
show,liger-method	show-methods
subsetLiger	subsetLiger
suggestK	suggestK
suggestLambda	suggestLambda
sumGroups	sumGroups
sumGroups.dgCMatrix	sumGroups
sumGroups.matrix	sumGroups
