rliger-package	rliger-package
$.liger	liger-class
$<-.liger	liger-class
%<>%	reexports
%>%	reexports
.complexHeatmapDotPlot	dot-complexHeatmapDotPlot
.ggCellViolin	dot-ggCellViolin
.ggplotLigerTheme	dot-ggplotLigerTheme
.ggScatter	dot-ggScatter
.plotHeatmap	dot-plotHeatmap
alignFactors	alignFactors
alignFactors.liger	alignFactors
alignFactors.Seurat	alignFactors
as.liger	as.liger
as.liger.dgCMatrix	as.liger
as.liger.Seurat	as.liger
as.liger.SingleCellExperiment	as.liger
as.ligerDataset	as.ligerDataset
as.ligerDataset.default	as.ligerDataset
as.ligerDataset.ligerDataset	as.ligerDataset
as.ligerDataset.matrix	as.ligerDataset
as.ligerDataset.Seurat	as.ligerDataset
as.ligerDataset.SingleCellExperiment	as.ligerDataset
bmmc	bmmc
c.liger	liger-class
calcAgreement	calcAgreement
calcAlignment	calcAlignment
calcARI	calcARI
calcDatasetSpecificity	calcDatasetSpecificity
calcNMI	calcNMI
calcPurity	calcPurity
cbind.ligerDataset	ligerDataset-class
cellMeta	liger-class
cellMeta,liger,character-method	liger-class
cellMeta,liger,missing-method	liger-class
cellMeta,liger,NULL-method	liger-class
cellMeta<-	liger-class
cellMeta<-,liger,character-method	liger-class
cellMeta<-,liger,missing-method	liger-class
centroidAlign	centroidAlign
centroidAlign.liger	centroidAlign
centroidAlign.Seurat	centroidAlign
closeAllH5	closeAllH5
closeAllH5.liger	closeAllH5
closeAllH5.ligerDataset	closeAllH5
commandDiff	commandDiff
commands	liger-class
commands,liger-method	liger-class
convertOldLiger	convertOldLiger
coordinate	coordinate
coordinate,liger,character-method	coordinate
coordinate,ligerSpatialDataset,missing-method	coordinate
coordinate<-	coordinate
coordinate<-,liger,character-method	coordinate
coordinate<-,ligerSpatialDataset,missing-method	coordinate
createH5LigerDataset	createH5LigerDataset
createLiger	createLiger
createLigerDataset	createLigerDataset
dataset	liger-class
dataset,liger,character_OR_NULL-method	liger-class
dataset,liger,missing-method	liger-class
dataset,liger,numeric-method	liger-class
dataset<-	liger-class
dataset<-,liger,character,ANY,ANY,matrixLike-method	liger-class
dataset<-,liger,character,missing,ANY,ligerDataset-method	liger-class
dataset<-,liger,character,missing,ANY,NULL-method	liger-class
datasets	liger-class
datasets,liger-method	liger-class
datasets<-	liger-class
datasets<-,liger,logical-method	liger-class
datasets<-,liger,missing-method	liger-class
defaultCluster	liger-class
defaultCluster,liger-method	liger-class
defaultCluster<-	liger-class
defaultCluster<-,liger,ANY,ANY,character-method	liger-class
defaultCluster<-,liger,ANY,ANY,factor-method	liger-class
defaultCluster<-,liger,ANY,ANY,NULL-method	liger-class
defaultDimRed	liger-class
defaultDimRed,liger-method	liger-class
defaultDimRed<-	liger-class
defaultDimRed<-,liger,character-method	liger-class
deg.marker	deg.marker
deg.pw	deg.pw
dim,liger-method	liger-class
dim,ligerDataset-method	ligerDataset-class
dimnames,liger-method	liger-class
dimnames,ligerDataset-method	ligerDataset-class
dimnames<-,liger,list-method	liger-class
dimnames<-,ligerDataset,list-method	ligerDataset-class
dimRed	liger-class
dimRed,liger,index-method	liger-class
dimRed,liger,missing_OR_NULL-method	liger-class
dimRed<-	liger-class
dimRed<-,liger,character,ANY,ANY,matrixLike-method	liger-class
dimRed<-,liger,index,ANY,ANY,NULL-method	liger-class
dimReds	liger-class
dimReds,liger-method	liger-class
dimReds<-	liger-class
dimReds<-,liger,list-method	liger-class
downsample	downsample
exportInteractTrack	exportInteractTrack
featureMeta	ligerDataset-class
featureMeta,ligerDataset-method	ligerDataset-class
featureMeta<-	ligerDataset-class
featureMeta<-,ligerDataset-method	ligerDataset-class
fortify.liger	liger-class
getFactorMarkers	getFactorMarkers
getH5File	ligerDataset-class
getH5File,liger,ANY-method	liger-class
getH5File,ligerDataset,missing-method	ligerDataset-class
getMatrix	ligerDataset-class
getMatrix,liger,ANY,ANY,ANY-method	liger-class
getMatrix,ligerATACDataset,ANY,missing,missing-method	ligerDataset-class
getMatrix,ligerDataset,ANY,missing,missing-method	ligerDataset-class
getProportionMito	getProportionMito
H5Apply	H5Apply
h5fileInfo	ligerDataset-class
h5fileInfo,ligerDataset-method	ligerDataset-class
h5fileInfo<-	ligerDataset-class
h5fileInfo<-,ligerDataset-method	ligerDataset-class
importBMMC	importVignetteData
importCGE	importVignetteData
importPBMC	importVignetteData
imputeKNN	imputeKNN
is.newLiger	is.newLiger
isH5Liger	isH5Liger
length.liger	liger-class
lengths.liger	liger-class
liger	liger-class
liger-class	liger-class
ligerATACDataset	ligerATACDataset-class
ligerATACDataset-class	ligerATACDataset-class
ligerCommand	ligerCommand-class
ligerCommand-class	ligerCommand-class
ligerDataset	ligerDataset-class
ligerDataset-class	ligerDataset-class
ligerMethDataset	ligerMethDataset-class
ligerMethDataset-class	ligerMethDataset-class
ligerRNADataset	ligerRNADataset-class
ligerRNADataset-class	ligerRNADataset-class
ligerSpatialDataset	ligerSpatialDataset-class
ligerSpatialDataset-class	ligerSpatialDataset-class
ligerToSeurat	ligerToSeurat
linkGenesAndPeaks	linkGenesAndPeaks
louvainCluster	rliger-deprecated
louvainCluster-deprecated	louvainCluster-deprecated
makeFeatureMatrix	makeFeatureMatrix
makeInteractTrack	rliger-deprecated
makeInteractTrack-deprecated	makeInteractTrack-deprecated
makeRiverplot	rliger-deprecated
makeRiverplot-deprecated	makeRiverplot-deprecated
mapCellMeta	mapCellMeta
mergeDenseAll	mergeSparseAll
mergeH5	mergeH5
mergeSparseAll	mergeSparseAll
modalOf	modalOf
names.liger	liger-class
names<-.liger	liger-class
normalize	normalize
normalize.DelayedArray	normalize
normalize.dgCMatrix	normalize
normalize.liger	normalize
normalize.ligerDataset	normalize
normalize.matrix	normalize
normalize.Seurat	normalize
normalizePeak	normalize
normData	ligerDataset-class
normData,liger-method	liger-class
normData,ligerDataset-method	ligerDataset-class
normData<-	ligerDataset-class
normData<-,liger,ANY,ANY,H5D-method	liger-class
normData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	liger-class
normData<-,ligerDataset,ANY,ANY,H5D-method	ligerDataset-class
normData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	ligerDataset-class
normPeak	peak
normPeak,liger,character-method	peak
normPeak,ligerATACDataset,missing-method	peak
normPeak<-	peak
normPeak<-,liger,character-method	peak
normPeak<-,ligerATACDataset,missing-method	peak
online_iNMF	rliger-deprecated
online_iNMF-deprecated	online_iNMF-deprecated
optimizeALS	rliger-deprecated
optimizeALS-deprecated	optimizeALS-deprecated
optimizeNewData	optimizeNewData
optimizeNewK	optimizeNewK
optimizeNewLambda	optimizeNewLambda
optimizeSubset	optimizeSubset
pbmc	pbmc
pbmcPlot	pbmcPlot
plotBarcodeRank	plotBarcodeRank
plotByDatasetAndCluster	plotDimRed
plotCellViolin	plotCellViolin
plotClusterDimRed	plotDimRed
plotClusterFactorDot	plotClusterFactorDot
plotClusterGeneDot	plotClusterGeneDot
plotClusterGeneViolin	plotClusterGeneViolin
plotClusterProportions	plotProportion
plotDatasetDimRed	plotDimRed
plotDensityDimRed	plotDensityDimRed
plotDimRed	plotDimRed
plotEnhancedVolcano	plotEnhancedVolcano
plotFactorDimRed	plotDimRed
plotFactorHeatmap	plotHeatmap
plotGeneDetectedViolin	plotViolin
plotGeneDimRed	plotDimRed
plotGeneHeatmap	plotHeatmap
plotGeneLoadingRank	plotGeneLoadings
plotGeneLoadings	plotGeneLoadings
plotGeneViolin	plotViolin
plotGODot	plotGODot
plotGroupClusterDimRed	plotGroupClusterDimRed
plotMarkerHeatmap	plotMarkerHeatmap
plotPairwiseDEGHeatmap	plotPairwiseDEGHeatmap
plotPeakDimRed	plotDimRed
plotProportion	plotProportion
plotProportionBar	plotProportion
plotProportionBox	plotProportionBox
plotProportionDot	plotProportion
plotProportionPie	plotProportion
plotSankey	plotSankey
plotSpatial2D	plotSpatial
plotSpatial2D.liger	plotSpatial
plotSpatial2D.ligerSpatialDataset	plotSpatial
plotTotalCountViolin	plotViolin
plotVarFeatures	plotVarFeatures
plotVolcano	plotVolcano
quantileAlignSNF	quantileAlignSNF
quantileNorm	quantileNorm
quantileNorm.liger	quantileNorm
quantileNorm.Seurat	quantileNorm
quantile_norm	rliger-deprecated
quantile_norm-deprecated	quantile_norm-deprecated
rawData	ligerDataset-class
rawData,liger-method	liger-class
rawData,ligerDataset-method	ligerDataset-class
rawData<-	ligerDataset-class
rawData<-,liger,ANY,ANY,H5D-method	liger-class
rawData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	liger-class
rawData<-,ligerDataset,ANY,ANY,H5D-method	ligerDataset-class
rawData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	ligerDataset-class
rawPeak	peak
rawPeak,liger,character-method	peak
rawPeak,ligerATACDataset,missing-method	peak
rawPeak<-	peak
rawPeak<-,liger,character-method	peak
rawPeak<-,ligerATACDataset,missing-method	peak
read10X	read10X
read10XATAC	read10X
read10XFiles	read10XFiles
read10XH5	read10XH5
read10XH5Delay	read10XH5
read10XH5Mem	read10XH5
read10XRNA	read10X
readH5AD	readH5AD
readH5ADDelay	readH5AD
readH5ADMem	readH5AD
readLiger	readLiger
readSubset	readSubset
reexports	reexports
removeMissing	removeMissing
removeMissingObs	removeMissing
restoreH5Liger	restoreH5Liger
restoreOnlineLiger	restoreH5Liger
retrieveCellFeature	retrieveCellFeature
reverseMethData	reverseMethData
rliger	rliger-package
rliger-deprecated	rliger-deprecated
runCINMF	runCINMF
runCINMF.liger	runCINMF
runCINMF.Seurat	runCINMF
runCluster	runCluster
runGeneralQC	runGeneralQC
runGOEnrich	runGOEnrich
runGSEA	runGSEA
runINMF	runINMF
runINMF.liger	runINMF
runINMF.Seurat	runINMF
runIntegration	runIntegration
runIntegration.liger	runIntegration
runIntegration.Seurat	runIntegration
runMarkerDEG	liger-DEG
runOnlineINMF	runOnlineINMF
runOnlineINMF.liger	runOnlineINMF
runOnlineINMF.Seurat	runOnlineINMF
runPairwiseDEG	liger-DEG
runTSNE	runTSNE
runUINMF	runUINMF
runUINMF.liger	runUINMF
runUMAP	runUMAP
runWilcoxon	liger-DEG
scaleData	ligerDataset-class
scaleData,liger,ANY-method	liger-class
scaleData,ligerDataset,missing-method	ligerDataset-class
scaleData<-	ligerDataset-class
scaleData<-,liger,ANY,ANY,H5D-method	liger-class
scaleData<-,liger,ANY,ANY,H5Group-method	liger-class
scaleData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	liger-class
scaleData<-,ligerDataset,ANY,ANY,H5D-method	ligerDataset-class
scaleData<-,ligerDataset,ANY,ANY,H5Group-method	ligerDataset-class
scaleData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method	ligerDataset-class
scaleNotCenter	scaleNotCenter
scaleNotCenter.DelayedArray	scaleNotCenter
scaleNotCenter.dgCMatrix	scaleNotCenter
scaleNotCenter.liger	scaleNotCenter
scaleNotCenter.ligerDataset	scaleNotCenter
scaleNotCenter.ligerMethDataset	scaleNotCenter
scaleNotCenter.Seurat	scaleNotCenter
scaleUnsharedData	ligerDataset-class
scaleUnsharedData,liger,character-method	liger-class
scaleUnsharedData,liger,numeric-method	liger-class
scaleUnsharedData,ligerDataset,missing-method	ligerDataset-class
scaleUnsharedData<-	ligerDataset-class
scaleUnsharedData<-,liger,ANY,ANY,H5D-method	liger-class
scaleUnsharedData<-,liger,ANY,ANY,H5Group-method	liger-class
scaleUnsharedData<-,liger,ANY,ANY,matrixLike_OR_NULL-method	liger-class
scaleUnsharedData<-,ligerDataset,missing,ANY,H5D-method	ligerDataset-class
scaleUnsharedData<-,ligerDataset,missing,ANY,H5Group-method	ligerDataset-class
scaleUnsharedData<-,ligerDataset,missing,ANY,matrixLike_OR_NULL-method	ligerDataset-class
selectBatchHVG	selectBatchHVG
selectBatchHVG.DelayedArray	selectBatchHVG
selectBatchHVG.dgCMatrix	selectBatchHVG
selectBatchHVG.liger	selectBatchHVG
selectBatchHVG.ligerDataset	selectBatchHVG
selectGenes	selectGenes
selectGenes.liger	selectGenes
selectGenes.Seurat	selectGenes
selectGenesVST	selectGenesVST
seuratToLiger	as.liger
show,liger-method	liger-class
show,ligerCommand-method	ligerCommand-class
show,ligerDataset-method	ligerDataset-class
sub-liger	sub-liger
sub-ligerDataset	sub-ligerDataset
sub-sub-liger	sub-sub-liger
subsetH5LigerDataset	subsetLigerDataset
subsetLiger	subsetLiger
subsetLigerDataset	subsetLigerDataset
subsetMemLigerDataset	subsetLigerDataset
suggestK	suggestK
updateLigerObject	updateLigerObject
varFeatures	liger-class
varFeatures,liger-method	liger-class
varFeatures<-	liger-class
varFeatures<-,liger,ANY,character-method	liger-class
varUnsharedFeatures	liger-class
varUnsharedFeatures,liger,ANY-method	liger-class
varUnsharedFeatures,ligerDataset,missing-method	liger-class
varUnsharedFeatures<-	liger-class
varUnsharedFeatures<-,liger,ANY,ANY,character-method	liger-class
varUnsharedFeatures<-,ligerDataset,missing,ANY,character-method	liger-class
writeH5	writeH5
writeH5.default	writeH5
writeH5.dgCMatrix	writeH5
writeH5.liger	writeH5
writeH5.ligerDataset	writeH5
writeH5AD	writeH5AD
writeH5AD.dgCMatrix	writeH5AD
writeH5AD.liger	writeH5AD
writeH5AD.ligerDataset	writeH5AD
[.liger	sub-liger
[.ligerDataset	sub-ligerDataset
[[.liger	sub-sub-liger
[[<-.liger	liger-class
