API for gcday/seurat_fresh
Tools for Single Cell Genomics

Global functions
ALRAChooseKPlot	Man page
AddMetaData	Man page
AddMetaData.Assay	Man page
AddMetaData.Seurat	Man page
AddModuleScore	Man page
AddSamples	Man page
AnchorSet	Man page
AnchorSet-class	Man page
Assay	Man page
Assay-class	Man page
AugmentPlot	Man page
AverageExpression	Man page
BarcodeInflectionsPlot	Man page
BlackAndWhite	Man page
BlueAndRed	Man page
BoldTitle	Man page
BuildClusterTree	Man page
CalculateBarcodeInflections	Man page
CaseMatch	Man page
CellCycleScoring	Man page
CellPlot	Man page
CellScatter	Man page
CellSelector	Man page
Cells	Man page
Cells.DimReduc	Man page
Cells.default	Man page
CollapseSpeciesExpressionMatrix	Man page
CombinePlots	Man page
Command	Man page
Command.Seurat	Man page
CreateAssayObject	Man page
CreateDimReducObject	Man page
CreateGeneActivityMatrix	Man page
CreateSeuratObject	Man page
CustomDistance	Man page
CustomPalette	Man page
DarkTheme	Man page
DefaultAssay	Man page
DefaultAssay.DimReduc	Man page
DefaultAssay.Seurat	Man page
DefaultAssay<-	Man page
DefaultAssay<-.Seurat	Man page
DietSeurat	Man page
DimHeatmap	Man page
DimPlot	Man page
DimReduc	Man page
DimReduc-class	Man page
DoHeatmap	Man page
DotPlot	Man page
ElbowPlot	Man page
Embeddings	Man page
Embeddings.DimReduc	Man page
Embeddings.Seurat	Man page
ExpMean	Man page
ExpSD	Man page
ExpVar	Man page
ExportToCellbrowser	Man page
FeatureHeatmap	Man page
FeatureLocator	Man page
FeaturePlot	Man page
FeatureScatter	Man page
FetchData	Man page
FindAllMarkers	Man page
FindAllMarkersNode	Man page
FindClusters	Man page
FindClusters.Seurat	Man page
FindClusters.default	Man page
FindConservedMarkers	Man page
FindIntegrationAnchors	Man page
FindMarkers	Man page
FindMarkers.Seurat	Man page
FindMarkers.default	Man page
FindMarkersNode	Man page
FindNeighbors	Man page
FindNeighbors.Assay	Man page
FindNeighbors.Seurat	Man page
FindNeighbors.default	Man page
FindNeighbors.dist	Man page
FindTransferAnchors	Man page
FindVariableFeatures	Man page
FindVariableFeatures.Assay	Man page
FindVariableFeatures.Seurat	Man page
FindVariableFeatures.default	Man page
FindVariableGenes	Man page
FontSize	Man page
GenePlot	Man page
GetAssay	Man page
GetAssay.Seurat	Man page
GetAssayData	Man page
GetAssayData.Assay	Man page
GetAssayData.Seurat	Man page
GetIntegrationData	Man page
GetResidual	Man page
Graph	Man page
Graph-class	Man page
HTODemux	Man page
HTOHeatmap	Man page
HVFInfo	Man page
HVFInfo.Assay	Man page
HVFInfo.Seurat	Man page
HoverLocator	Man page
ICAPlot	Man page
Idents	Man page
Idents.Seurat	Man page
Idents<-	Man page
Idents<-.Seurat	Man page
IntegrateData	Man page
IntegrationData	Man page
IntegrationData-class	Man page
JS	Man page
JS.DimReduc	Man page
JS.JackStrawData	Man page
JS<-	Man page
JS<-.DimReduc	Man page
JS<-.JackStrawData	Man page
JackStraw	Man page
JackStrawData	Man page
JackStrawData-class	Man page
JackStrawPlot	Man page
Key	Man page
Key.Assay	Man page
Key.DimReduc	Man page
Key.Seurat	Man page
Key<-	Man page
Key<-.Assay	Man page
Key<-.DimReduc	Man page
L2CCA	Man page
L2Dim	Man page
LabelClusters	Man page
LabelPoints	Man page
Labeler	Man page
Loadings	Man page
Loadings.DimReduc	Man page
Loadings.Seurat	Man page
Loadings<-	Man page
Loadings<-.DimReduc	Man page
LocalStruct	Man page
LogNormalize	Man page
LogSeuratCommand	Man page
LogVMR	Man page
MULTIseqDemux	Man page
MeanVarPlot	Man page
MergeSeurat	Man page
MetaFeature	Man page
MinMax	Man page
Misc	Man page
Misc.Assay	Man page
Misc.Seurat	Man page
Misc<-	Man page
Misc<-.Assay	Man page
Misc<-.Seurat	Man page
MixingMetric	Man page
NoAxes	Man page
NoGrid	Man page
NoLegend	Man page
NormalizeData	Man page
NormalizeData.Assay	Man page
NormalizeData.Seurat	Man page
NormalizeData.default	Man page
OldWhichCells	Man page
OldWhichCells.Assay	Man page
OldWhichCells.Seurat	Man page
PCAPlot	Man page
PCASigGenes	Man page
PCHeatmap	Man page
PercentageFeatureSet	Man page
PlotClusterTree	Man page
PolyDimPlot	Man page
PolyFeaturePlot	Man page
Project	Man page
Project.Seurat	Man page
Project<-	Man page
Project<-.Seurat	Man page
ProjectDim	Man page
PurpleAndYellow	Man page
Read10X	Man page
Read10X_h5	Man page
ReadAlevin	Man page
ReadAlevinCsv	Man page
ReadH5AD	Man page
ReadH5AD.H5File	Man page
ReadH5AD.character	Man page
RelativeCounts	Man page
RenameCells	Man page
RenameCells.Assay	Man page
RenameCells.DimReduc	Man page
RenameCells.Seurat	Man page
RenameIdent	Man page
RenameIdents	Man page
RenameIdents.Seurat	Man page
ReorderIdent	Man page
ReorderIdent.Seurat	Man page
RestoreLegend	Man page
RidgePlot	Man page
RotatedAxis	Man page
RunALRA	Man page
RunALRA.Seurat	Man page
RunALRA.default	Man page
RunCCA	Man page
RunCCA.Seurat	Man page
RunCCA.default	Man page
RunICA	Man page
RunICA.Assay	Man page
RunICA.Seurat	Man page
RunICA.default	Man page
RunLSI	Man page
RunLSI.Assay	Man page
RunLSI.Seurat	Man page
RunLSI.default	Man page
RunPCA	Man page
RunPCA.Assay	Man page
RunPCA.Seurat	Man page
RunPCA.default	Man page
RunTSNE	Man page
RunTSNE.DimReduc	Man page
RunTSNE.Seurat	Man page
RunTSNE.dist	Man page
RunTSNE.matrix	Man page
RunUMAP	Man page
RunUMAP.Graph	Man page
RunUMAP.Seurat	Man page
RunUMAP.default	Man page
SCTransform	Man page
SampleUMI	Man page
ScaleData	Man page
ScaleData.Assay	Man page
ScaleData.Seurat	Man page
ScaleData.default	Man page
ScoreJackStraw	Man page
ScoreJackStraw.DimReduc	Man page
ScoreJackStraw.JackStrawData	Man page
ScoreJackStraw.Seurat	Man page
SelectIntegrationFeatures	Man page
SetAssayData	Man page
SetAssayData.Assay	Man page
SetAssayData.Seurat	Man page
SetDimReduction	Man page
SetIdent	Man page
SetIdent.Seurat	Man page
SetIntegrationData	Man page
Seurat	Man page
Seurat-class	Man page
Seurat-package	Man page
SeuratAccess	Man page
SeuratAxes	Man page
SeuratCommand	Man page
SeuratCommand-class	Man page
SeuratTheme	Man page
SpatialTheme	Man page
SplitDotPlotGG	Man page
SplitObject	Man page
StashIdent	Man page
StashIdent.Seurat	Man page
Stdev	Man page
Stdev.DimReduc	Man page
Stdev.Seurat	Man page
StopCellbrowser	Man page
SubsetByBarcodeInflections	Man page
SubsetData	Man page
SubsetData.Assay	Man page
SubsetData.Seurat	Man page
TF.IDF	Man page
TSNEPlot	Man page
Tool	Man page
Tool.Seurat	Man page
Tool<-	Man page
Tool<-.Seurat	Man page
Tools	Man page
TopCells	Man page
TopFeatures	Man page
TransferData	Man page
UMAPPlot	Man page
UpdateSeuratObject	Man page
VariableFeaturePlot	Man page
VariableFeatures	Man page
VariableFeatures.Assay	Man page
VariableFeatures.Seurat	Man page
VariableFeatures<-	Man page
VariableFeatures<-.Assay	Man page
VariableFeatures<-.Seurat	Man page
VariableGenePlot	Man page
VizDimLoadings	Man page
VlnPlot	Man page
WhichCells	Man page
WhichCells.Assay	Man page
WhichCells.Seurat	Man page
WhiteBackground	Man page
WriteH5AD	Man page
WriteH5AD.Seurat	Man page
[.Seurat	Man page
[[<-,Assay-method	Man page
[[<-,Seurat-method	Man page
as.CellDataSet	Man page
as.CellDataSet.Seurat	Man page
as.Graph	Man page
as.Graph.Matrix	Man page
as.Graph.matrix	Man page
as.Seurat	Man page
as.Seurat.CellDataSet	Man page
as.Seurat.SingleCellExperiment	Man page
as.Seurat.loom	Man page
as.SingleCellExperiment	Man page
as.SingleCellExperiment.Seurat	Man page
as.data.frame.Matrix	Man page
as.list.SeuratCommand	Man page
as.loom	Man page
as.loom.Seurat	Man page
as.sparse	Man page
as.sparse.H5Group	Man page
as.sparse.Matrix	Man page
as.sparse.data.frame	Man page
as.sparse.matrix	Man page
cc.genes	Man page
levels.Seurat	Man page
levels<-.Seurat	Man page
merge	Man page
merge.Assay	Man page
merge.Seurat	Man page
pbmc_small	Man page
print	Man page
print.DimReduc	Man page
seurat	Man page
seurat-class	Man page
subset	Man page
subset.Seurat	Man page