Seurat-package	Seurat-package
%iff%	reexports
%||%	reexports
AddAzimuthResults	AddAzimuthResults
AddAzimuthScores	AddAzimuthScores
AddMetaData	reexports
AddModuleScore	AddModuleScore
AggregateExpression	AggregateExpression
AnchorSet	AnchorSet-class
AnchorSet-class	AnchorSet-class
AnnotateAnchors	AnnotateAnchors
AnnotateAnchors.default	AnnotateAnchors
AnnotateAnchors.IntegrationAnchorSet	AnnotateAnchors
AnnotateAnchors.TransferAnchorSet	AnnotateAnchors
as.CellDataSet	as.CellDataSet
as.CellDataSet.Seurat	as.CellDataSet
as.data.frame.Matrix	as.sparse
as.Graph	reexports
as.Neighbor	reexports
as.Seurat	reexports
as.Seurat.CellDataSet	as.Seurat
as.Seurat.SingleCellExperiment	as.Seurat
as.SingleCellExperiment	as.SingleCellExperiment
as.SingleCellExperiment.Seurat	as.SingleCellExperiment
as.sparse	reexports
as.sparse.H5Group	as.sparse
Assay-class	Assay-class
Assays	reexports
AugmentPlot	AugmentPlot
AutoPointSize	AutoPointSize
AverageExpression	AverageExpression
BarcodeInflectionsPlot	BarcodeInflectionsPlot
BGTextColor	BGTextColor
BlackAndWhite	CustomPalette
BlueAndRed	CustomPalette
BoldTitle	SeuratTheme
BridgeCellsRepresentation	BridgeCellsRepresentation
BridgeReferenceSet	BridgeReferenceSet-class
BridgeReferenceSet-class	BridgeReferenceSet-class
BuildClusterTree	BuildClusterTree
BuildNicheAssay	BuildNicheAssay
CalcDispersion	CalcDispersion
CalcPerturbSig	CalcPerturbSig
CalculateBarcodeInflections	CalculateBarcodeInflections
CaseMatch	CaseMatch
cc.genes	cc.genes
cc.genes.updated.2019	cc.genes.updated.2019
CCAIntegration	CCAIntegration
CellCycleScoring	CellCycleScoring
CellPlot	CellScatter
Cells	reexports
Cells.SCTModel	Cells
Cells.SlideSeq	Cells
Cells.STARmap	Cells
Cells.VisiumV1	Cells
CellsByIdentities	reexports
CellsByImage	CellsByImage
CellScatter	CellScatter
CellSelector	CellSelector
CenterTitle	SeuratTheme
CollapseEmbeddingOutliers	CollapseEmbeddingOutliers
CollapseSpeciesExpressionMatrix	CollapseSpeciesExpressionMatrix
ColorDimSplit	ColorDimSplit
CombinePlots	CombinePlots
Command	reexports
components	reexports
contrast-theory	contrast-theory
CountSketch	CountSketch
CreateAssayObject	reexports
CreateCategoryMatrix	CreateCategoryMatrix
CreateDimReducObject	reexports
CreateSCTAssayObject	CreateSCTAssayObject
CreateSeuratObject	reexports
CustomDistance	CustomDistance
CustomPalette	CustomPalette
DarkTheme	SeuratTheme
DEenrichRPlot	DEenrichRPlot
DefaultAssay	reexports
DefaultAssay<-	reexports
DietSeurat	DietSeurat
DimHeatmap	DimHeatmap
DimPlot	DimPlot
DimReduc-class	DimReduc-class
DiscretePalette	DiscretePalette
DISP	DISP
Distances	reexports
DoHeatmap	DoHeatmap
DotPlot	DotPlot
ElbowPlot	ElbowPlot
Embeddings	reexports
ExpMean	ExpMean
ExpSD	ExpSD
ExpVar	ExpVar
FastRowScale	FastRowScale
FastRPCAIntegration	FastRPCAIntegration
FeatureHeatmap	FeaturePlot
FeatureLocator	CellSelector
FeaturePlot	FeaturePlot
FeatureScatter	FeatureScatter
FetchData	reexports
FetchResiduals	FetchResiduals
FetchResidualSCTModel	FetchResidualSCTModel
FetchResiduals_reference	FetchResiduals_reference
FilterSlideSeq	FilterSlideSeq
FindAllMarkers	FindAllMarkers
FindAllMarkersNode	FindAllMarkers
FindBridgeAnchor	FindBridgeAnchor
FindBridgeIntegrationAnchors	FindBridgeIntegrationAnchors
FindBridgeTransferAnchors	FindBridgeTransferAnchors
FindClusters	FindClusters
FindClusters.default	FindClusters
FindClusters.Seurat	FindClusters
FindConservedMarkers	FindConservedMarkers
FindIntegrationAnchors	FindIntegrationAnchors
FindMarkers	FindMarkers
FindMarkers.Assay	FindMarkers
FindMarkers.default	FindMarkers
FindMarkers.DimReduc	FindMarkers
FindMarkers.SCTAssay	FindMarkers
FindMarkers.Seurat	FindMarkers
FindMarkersNode	FindMarkers
FindMultiModalNeighbors	FindMultiModalNeighbors
FindNeighbors	FindNeighbors
FindNeighbors.Assay	FindNeighbors
FindNeighbors.default	FindNeighbors
FindNeighbors.dist	FindNeighbors
FindNeighbors.Seurat	FindNeighbors
FindSpatiallyVariableFeatures	FindSpatiallyVariableFeatures
FindSpatiallyVariableFeatures.Assay	FindSpatiallyVariableFeatures
FindSpatiallyVariableFeatures.default	FindSpatiallyVariableFeatures
FindSpatiallyVariableFeatures.Seurat	FindSpatiallyVariableFeatures
FindSpatiallyVariableFeatures.StdAssay	FindSpatiallyVariableFeatures
FindSubCluster	FindSubCluster
FindTransferAnchors	FindTransferAnchors
FindVariableFeatures	FindVariableFeatures
FindVariableFeatures.Assay	FindVariableFeatures
FindVariableFeatures.SCTAssay	FindVariableFeatures
FindVariableFeatures.Seurat	FindVariableFeatures
FindVariableFeatures.V3Matrix	FindVariableFeatures
FindVariableGenes	FindVariableFeatures
FoldChange	FoldChange
FoldChange.Assay	FoldChange
FoldChange.default	FoldChange
FoldChange.DimReduc	FoldChange
FoldChange.SCTAssay	FoldChange
FoldChange.Seurat	FoldChange
FontSize	SeuratTheme
fortify	fortify-Spatial
fortify-Spatial	fortify-Spatial
fortify.Centroids	fortify-Spatial
fortify.Molecules	fortify-Spatial
fortify.Segmentation	fortify-Spatial
GaussianSketch	GaussianSketch
GenePlot	FeatureScatter
GeneSymbolThesarus	UpdateSymbolList
GetAssay	GetAssay
GetAssay.Seurat	GetAssay
GetAssayData	reexports
GetImage	reexports
GetImage.SlideSeq	GetImage
GetImage.STARmap	GetImage
GetImage.VisiumV1	GetImage
GetIntegrationData	GetIntegrationData
GetResidual	GetResidual
GetTissueCoordinates	reexports
GetTissueCoordinates.SlideSeq	GetTissueCoordinates
GetTissueCoordinates.STARmap	GetTissueCoordinates
GetTissueCoordinates.VisiumV1	GetTissueCoordinates
GetTransferPredictions	GetTransferPredictions
Graph-class	Graph-class
GroupCorrelation	GroupCorrelation
GroupCorrelationPlot	GroupCorrelationPlot
HarmonyIntegration	HarmonyIntegration
HoverLocator	HoverLocator
HTODemux	HTODemux
HTOHeatmap	HTOHeatmap
HVFInfo	reexports
HVFInfo.SCTAssay	HVFInfo.SCTAssay
ICAPlot	DimPlot
Idents	reexports
Idents<-	reexports
IFeaturePlot	IFeaturePlot
ImageDimPlot	ImageDimPlot
ImageFeaturePlot	ImageFeaturePlot
Images	reexports
Index	reexports
Index<-	reexports
Indices	reexports
IntegrateData	IntegrateData
IntegrateEmbeddings	IntegrateEmbeddings
IntegrateEmbeddings.IntegrationAnchorSet	IntegrateEmbeddings
IntegrateEmbeddings.TransferAnchorSet	IntegrateEmbeddings
IntegrateLayers	IntegrateLayers
IntegrationAnchorSet	IntegrationAnchorSet-class
IntegrationAnchorSet-class	IntegrationAnchorSet-class
IntegrationData	IntegrationData-class
IntegrationData-class	IntegrationData-class
Intensity	contrast-theory
IsGlobal	reexports
ISpatialDimPlot	ISpatialDimPlot
ISpatialFeaturePlot	ISpatialFeaturePlot
JackStraw	JackStraw
JackStrawData-class	JackStrawData-class
JackStrawPlot	JackStrawPlot
JointPCAIntegration	JointPCAIntegration
JS	reexports
JS<-	reexports
Key	reexports
Key<-	reexports
L2CCA	L2CCA
L2Dim	L2Dim
LabelClusters	LabelClusters
Labeler	LabelPoints
LabelPoints	LabelPoints
levels.SCTAssay	SCTAssay-class
levels<-.SCTAssay	SCTAssay-class
LeverageScore	LeverageScore
LeverageScore.Assay	LeverageScore
LeverageScore.default	LeverageScore
LeverageScore.Seurat	LeverageScore
LeverageScore.StdAssay	LeverageScore
LinkedDimPlot	LinkedPlots
LinkedFeaturePlot	LinkedPlots
LinkedPlot	LinkedPlots
LinkedPlots	LinkedPlots
Load10X_Spatial	Load10X_Spatial
LoadAkoya	ReadAkoya
LoadAnnoyIndex	LoadAnnoyIndex
LoadCurioSeeker	LoadCurioSeeker
LoadHuBMAPCODEX	ReadVitessce
Loadings	reexports
Loadings<-	reexports
LoadNanostring	ReadNanostring
LoadSTARmap	LoadSTARmap
LoadVizgen	ReadVizgen
LoadXenium	ReadXenium
LocalStruct	LocalStruct
LogNormalize	LogNormalize
LogNormalize.data.frame	LogNormalize
LogNormalize.default	LogNormalize
LogNormalize.V3Matrix	LogNormalize
LogSeuratCommand	reexports
LogVMR	LogVMR
Luminance	contrast-theory
MappingScore	MappingScore
MappingScore.AnchorSet	MappingScore
MappingScore.default	MappingScore
MapQuery	MapQuery
MeanVarPlot	VariableFeaturePlot
merge.SCTAssay	merge.SCTAssay
MetaFeature	MetaFeature
MinMax	MinMax
Misc	reexports
Misc<-	reexports
MixingMetric	MixingMetric
MixscapeHeatmap	MixscapeHeatmap
MixscapeLDA	MixscapeLDA
ModalityWeights	ModalityWeights-class
ModalityWeights-class	ModalityWeights-class
MULTIseqDemux	MULTIseqDemux
MVP	MVP
Neighbor-class	Neighbor-class
Neighbors	reexports
NNPlot	NNPlot
NNtoGraph	NNtoGraph
NoAxes	SeuratTheme
NoGrid	SeuratTheme
NoLegend	SeuratTheme
NormalizeData	NormalizeData
NormalizeData.Assay	NormalizeData
NormalizeData.Seurat	NormalizeData
NormalizeData.V3Matrix	NormalizeData
PCAPlot	DimPlot
PCASigGenes	PCASigGenes
PCHeatmap	DimHeatmap
PercentAbove	PercentAbove
PercentageFeatureSet	PercentageFeatureSet
PlotClusterTree	PlotClusterTree
PlotPerturbScore	PlotPerturbScore
PolyDimPlot	PolyDimPlot
PolyFeaturePlot	PolyFeaturePlot
PredictAssay	PredictAssay
PrepareBridgeReference	PrepareBridgeReference
PrepLDA	PrepLDA
PrepSCTFindMarkers	PrepSCTFindMarkers
PrepSCTIntegration	PrepSCTIntegration
Project	reexports
Project<-	reexports
ProjectCellEmbeddings	ProjectCellEmbeddings
ProjectCellEmbeddings.Assay	ProjectCellEmbeddings
ProjectCellEmbeddings.default	ProjectCellEmbeddings
ProjectCellEmbeddings.IterableMatrix	ProjectCellEmbeddings
ProjectCellEmbeddings.SCTAssay	ProjectCellEmbeddings
ProjectCellEmbeddings.Seurat	ProjectCellEmbeddings
ProjectCellEmbeddings.StdAssay	ProjectCellEmbeddings
ProjectData	ProjectData
ProjectDim	ProjectDim
ProjectDimReduc	ProjectDimReduc
ProjectIntegration	ProjectIntegration
ProjectUMAP	ProjectUMAP
ProjectUMAP.default	ProjectUMAP
ProjectUMAP.DimReduc	ProjectUMAP
ProjectUMAP.Seurat	ProjectUMAP
PseudobulkExpression	PseudobulkExpression
PurpleAndYellow	CustomPalette
Radius	reexports
Radius.SlideSeq	Radius
Radius.STARmap	Radius
Radius.VisiumV1	Radius
Read10X	Read10X
Read10X_h5	Read10X_h5
Read10X_Image	Read10X_Image
Read10X_probe_metadata	Read10X_probe_metadata
ReadAkoya	ReadAkoya
ReadMtx	ReadMtx
ReadNanostring	ReadNanostring
ReadParseBio	ReadParseBio
ReadSlideSeq	ReadSlideSeq
ReadSTARsolo	ReadSTARsolo
ReadVitessce	ReadVitessce
ReadVizgen	ReadVizgen
ReadXenium	ReadXenium
Reductions	reexports
reexports	reexports
RegroupIdents	RegroupIdents
RelativeCounts	RelativeCounts
RenameCells	reexports
RenameCells.SCTAssay	RenameCells
RenameCells.SlideSeq	RenameCells
RenameCells.STARmap	RenameCells
RenameCells.VisiumV1	RenameCells
RenameIdents	reexports
ReorderIdent	reexports
RestoreLegend	SeuratTheme
RidgePlot	RidgePlot
RotatedAxis	SeuratTheme
RowMergeSparseMatrices	reexports
RPCAIntegration	RPCAIntegration
RunCCA	RunCCA
RunCCA.default	RunCCA
RunCCA.Seurat	RunCCA
RunGraphLaplacian	RunGraphLaplacian
RunGraphLaplacian.default	RunGraphLaplacian
RunGraphLaplacian.Seurat	RunGraphLaplacian
RunICA	RunICA
RunICA.Assay	RunICA
RunICA.default	RunICA
RunICA.Seurat	RunICA
RunLDA	RunLDA
RunLDA.Assay	RunLDA
RunLDA.default	RunLDA
RunLDA.Seurat	RunLDA
RunMarkVario	RunMarkVario
RunMixscape	RunMixscape
RunMoransI	RunMoransI
RunPCA	RunPCA
RunPCA.Assay	RunPCA
RunPCA.default	RunPCA
RunPCA.Seurat	RunPCA
RunSLSI	RunSLSI
RunSLSI.Assay	RunSLSI
RunSLSI.default	RunSLSI
RunSLSI.Seurat	RunSLSI
RunSPCA	RunSPCA
RunSPCA.Assay	RunSPCA
RunSPCA.Assay5	RunSPCA
RunSPCA.default	RunSPCA
RunSPCA.Seurat	RunSPCA
RunTSNE	RunTSNE
RunTSNE.DimReduc	RunTSNE
RunTSNE.dist	RunTSNE
RunTSNE.matrix	RunTSNE
RunTSNE.Seurat	RunTSNE
RunUMAP	RunUMAP
RunUMAP.default	RunUMAP
RunUMAP.Graph	RunUMAP
RunUMAP.Neighbor	RunUMAP
RunUMAP.Seurat	RunUMAP
SampleUMI	SampleUMI
SaveAnnoyIndex	SaveAnnoyIndex
ScaleData	ScaleData
ScaleData.Assay	ScaleData
ScaleData.default	ScaleData
ScaleData.IterableMatrix	ScaleData
ScaleData.Seurat	ScaleData
ScaleFactors	ScaleFactors
scalefactors	ScaleFactors
ScaleFactors.VisiumV1	ScaleFactors
ScoreJackStraw	ScoreJackStraw
ScoreJackStraw.DimReduc	ScoreJackStraw
ScoreJackStraw.JackStrawData	ScoreJackStraw
ScoreJackStraw.Seurat	ScoreJackStraw
SCTAssay	SCTAssay-class
SCTAssay-class	SCTAssay-class
SCTModel	SCTAssay-class
SCTransform	SCTransform
SCTransform.Assay	SCTransform
SCTransform.default	SCTransform
SCTransform.IterableMatrix	SCTransform
SCTransform.Seurat	SCTransform
SCTResults	SCTResults
SCTResults.SCTAssay	SCTResults
SCTResults.SCTModel	SCTResults
SCTResults.Seurat	SCTResults
SCTResults<-	SCTResults
SCTResults<-.SCTAssay	SCTResults
SCTResults<-.SCTModel	SCTResults
SelectIntegrationFeatures	SelectIntegrationFeatures
SelectIntegrationFeatures5	SelectIntegrationFeatures5
SelectSCTIntegrationFeatures	SelectSCTIntegrationFeatures
SetAssayData	reexports
SetIdent	reexports
SetIntegrationData	SetIntegrationData
SetQuantile	SetQuantile
Seurat	Seurat-package
Seurat-class	Seurat-class
SeuratAxes	SeuratTheme
SeuratCommand-class	SeuratCommand-class
SeuratTheme	SeuratTheme
SingleCorPlot	SingleCorPlot
SingleDimPlot	SingleDimPlot
SingleExIPlot	SingleExIPlot
SingleImageMap	SingleImageMap
SingleImagePlot	SingleImagePlot
SingleRasterMap	SingleRasterMap
SingleSpatialPlot	SingleSpatialPlot
SketchData	SketchData
SlideSeq	SlideSeq-class
SlideSeq-class	SlideSeq-class
SpatialDimPlot	SpatialPlot
SpatialFeaturePlot	SpatialPlot
SpatialImage-class	SpatialImage-class
SpatiallyVariableFeatures	reexports
SpatialPlot	SpatialPlot
SpatialTheme	SeuratTheme
SplitDotPlotGG	DotPlot
SplitObject	SplitObject
STARmap	STARmap-class
STARmap-class	STARmap-class
StashIdent	reexports
Stdev	reexports
subset.AnchorSet	subset.AnchorSet
SubsetByBarcodeInflections	SubsetByBarcodeInflections
SVFInfo	reexports
Tool	reexports
Tool<-	reexports
TopCells	TopCells
TopFeatures	TopFeatures
TopNeighbors	TopNeighbors
TransferAnchorSet	TransferAnchorSet-class
TransferAnchorSet-class	TransferAnchorSet-class
TransferData	TransferData
TransferSketchLabels	TransferSketchLabels
TSNEPlot	DimPlot
UMAPPlot	DimPlot
UnSketchEmbeddings	UnSketchEmbeddings
UpdateSCTAssays	UpdateSCTAssays
UpdateSeuratObject	reexports
UpdateSymbolList	UpdateSymbolList
VariableFeaturePlot	VariableFeaturePlot
VariableFeatures	reexports
VariableFeatures<-	reexports
VariableGenePlot	VariableFeaturePlot
VisiumV1	VisiumV1-class
VisiumV1-class	VisiumV1-class
VizDimLoadings	VizDimLoadings
VlnPlot	VlnPlot
VST	VST
VST.default	VST
VST.dgCMatrix	VST
VST.IterableMatrix	VST
VST.matrix	VST
WhichCells	reexports
WhiteBackground	SeuratTheme
writing-integration	writing-integration
