API for Seurat
Tools for Single Cell Genomics

Global functions
.AddMetaData Source code
.onAttach Source code
.onLoad Source code
ALRAChooseKPlot Man page Source code
AUCMarkerTest Source code
AddDatasetID Source code
AddMetaData Man page Source code
AddMetaData.Assay Man page Source code
AddMetaData.Seurat Man page Source code
AddModuleScore Man page Source code
AddSamples Man page
AdjustSampleTree Source code
AnchorSet Man page
AnchorSet-class Man page
AnnotateAnchors Source code
AnnoyBuildIndex Source code
AnnoyNN Source code
AnnoySearch Source code
Assay Man page
Assay-class Man page
Assays Man page Source code
AugmentPlot Man page Source code
AutoPointSize Source code
AverageExpression Man page Source code
BGTextColor Man page Source code
Bandwidth Source code
BarcodeInflectionsPlot Man page Source code
BinData Source code
BlackAndWhite Man page Source code
BlendExpression Source code
BlendMap Source code
BlendMatrix Source code
BlueAndRed Man page Source code
BoldTitle Man page Source code
BuildClusterTree Man page Source code
BuildSampleTree Source code
CalcN Source code
CalculateBarcodeInflections Man page Source code
CaseMatch Man page Source code
CellCycleScoring Man page Source code
CellPlot Man page
CellScatter Man page Source code
CellSelector Man page Source code
Cells Man page Source code
Cells.DimReduc Man page Source code
Cells.Neighbor Man page Source code
Cells.STARmap Man page Source code
Cells.SlideSeq Man page Source code
Cells.SpatialImage Man page Source code
Cells.VisiumV1 Man page Source code
Cells.default Man page Source code
CellsByIdentities Man page Source code
CellsByImage Man page Source code
CenterTitle Man page Source code
CheckDots Source code
CheckDuplicateCellNames Source code
CheckFeatures Source code
CheckGC Source code
ChunkPoints Source code
ClassifyCells Source code
Col2Hex Source code
CollapseEmbeddingOutliers Man page Source code
CollapseSpeciesExpressionMatrix Man page Source code
Collections Source code
ColorDimSplit Man page Source code
CombinePlots Man page Source code
Command Man page Source code
Command.Seurat Man page Source code
ComputeRMetric Source code
ComputeSNN Source code
ConstructNNMat Source code
CountAnchors Source code
CreateAnn Source code
CreateAssayObject Man page Source code
CreateDimReducObject Man page Source code
CreateGeneActivityMatrix Man page Source code
CreateSeuratObject Man page Source code
CreateSeuratObject.Assay Man page Source code
CreateSeuratObject.default Man page Source code
CustomDistance Man page Source code
CustomNormalize Source code
CustomPalette Man page Source code
DESeq2DETest Source code
DFT Source code
DarkTheme Man page Source code
DefaultAssay Man page Source code
DefaultAssay.Assay Man page Source code
DefaultAssay.DimReduc Man page Source code
DefaultAssay.Graph Man page Source code
DefaultAssay.Seurat Man page Source code
DefaultAssay.SeuratCommand Man page Source code
DefaultAssay.SpatialImage Man page Source code
DefaultAssay<- Man page
DefaultAssay<-.Seurat Man page
DefaultAssay<-.SpatialImage Man page
DefaultDimReduc Source code
DefaultImage Source code
DietSeurat Man page Source code
DiffExpTest Source code
DiffTTest Source code
DifferentialAUC Source code
DifferentialLRT Source code
DimHeatmap Man page Source code
DimPlot Man page Source code
DimReduc Man page
DimReduc-class Man page
DirectSNNToFile Source code
DiscretePalette Man page Source code
Distances Man page Source code
Distances.Neighbor Man page Source code
DoHeatmap Man page Source code
DotPlot Man page Source code
ElbowPlot Man page Source code
Embeddings Man page Source code
Embeddings.DimReduc Man page Source code
Embeddings.Seurat Man page Source code
EmpiricalP Source code
ExIPlot Source code
ExpMean Man page Source code
ExpSD Man page Source code
ExpVar Man page Source code
ExportToCellbrowser Man page Source code
Extend Source code
ExtractField Source code
FacetTheme Source code
FastCov Source code
FastCovMats Source code
FastExpMean Source code
FastLogVMR Source code
FastRBind Source code
FastRowScale Man page Source code
FastSparseRowScale Source code
FastSparseRowScaleWithKnownStats Source code
FeatureHeatmap Man page
FeatureLocator Man page Source code
FeaturePlot Man page Source code
FeatureScatter Man page Source code
FetchData Man page Source code
FilterAnchors Source code
FilterObjects Source code
FilterSlideSeq Man page Source code
FindAllMarkers Man page Source code
FindAllMarkersNode Man page
FindAnchorPairs Source code
FindAnchors Source code
FindClusters Man page Source code
FindClusters.Seurat Man page Source code
FindClusters.default Man page Source code
FindConservedMarkers Man page Source code
FindIntegrationAnchors Man page Source code
FindIntegrationMatrix Source code
FindMarkers Man page Source code
FindMarkers.Seurat Man page Source code
FindMarkers.default Man page Source code
FindMarkersNode Man page
FindNN Source code
FindNeighbors Man page Source code
FindNeighbors.Assay Man page Source code
FindNeighbors.Seurat Man page Source code
FindNeighbors.default Man page Source code
FindNeighbors.dist Man page Source code
FindObject Source code
FindSpatiallyVariableFeatures Man page Source code
FindSpatiallyVariableFeatures.Assay Man page Source code
FindSpatiallyVariableFeatures.Seurat Man page Source code
FindSpatiallyVariableFeatures.default Man page Source code
FindThresh Source code
FindTransferAnchors Man page Source code
FindVariableFeatures Man page Source code
FindVariableFeatures.Assay Man page Source code
FindVariableFeatures.Seurat Man page Source code
FindVariableFeatures.default Man page Source code
FindVariableGenes Man page
FindWeights Source code
FindWeightsC Source code
FontSize Man page Source code
GGpointToBase Source code
GGpointToPlotlyBuild Source code
GLMDETest Source code
GenePlot Man page
GeneSymbolThesarus Man page Source code
GetAllInternalNodes Source code
GetAssay Man page Source code
GetAssay.Seurat Man page Source code
GetAssayData Man page Source code
GetAssayData.Assay Man page Source code
GetAssayData.Seurat Man page Source code
GetCellOffsets Source code
GetColourAesthetics Source code
GetDescendants Source code
GetFeatureGroups Source code
GetImage Man page Source code
GetImage.STARmap Source code
GetImage.Seurat Man page Source code
GetImage.SlideSeq Source code
GetImage.SpatialImage Man page Source code
GetImage.VisiumV1 Man page Source code
GetIntegrationData Man page Source code
GetLeftDescendants Source code
GetResidual Man page Source code
GetResidualVstOut Source code
GetRightDescendants Source code
GetTissueCoordinates Man page Source code
GetTissueCoordinates.STARmap Source code
GetTissueCoordinates.Seurat Man page Source code
GetTissueCoordinates.SlideSeq Source code
GetTissueCoordinates.SpatialImage Man page Source code
GetTissueCoordinates.VisiumV1 Man page Source code
GetTransferPredictions Man page Source code
GetXYAesthetics Source code
Graph Man page
Graph-class Man page
GraphToNeighborHelper Source code
GroupCorrelation Man page Source code
GroupCorrelationPlot Man page Source code
GroupSingletons Source code
HTODemux Man page Source code
HTOHeatmap Man page Source code
HVFInfo Man page Source code
HVFInfo.Assay Man page Source code
HVFInfo.Seurat Man page Source code
HoverLocator Man page Source code
ICAPlot Man page
IFeaturePlot Man page Source code
ISpatialDimPlot Man page Source code
ISpatialFeaturePlot Man page Source code
Idents Man page Source code
Idents.Seurat Man page Source code
Idents<- Man page
Idents<-.Seurat Man page
Images Man page Source code
Index Man page Source code
Index.Neighbor Man page Source code
Index<- Man page
Index<-.Neighbor Man page
Indices Man page Source code
Indices.Neighbor Man page Source code
IntegrateData Man page Source code
IntegrateDataC Source code
IntegrationData Man page
IntegrationData-class Man page
Intensity Man page Source code
Interleave Source code
InvertCoordinate Source code
InvertHex Source code
IsGlobal Man page Source code
IsGlobal.DimReduc Man page Source code
IsGlobal.SpatialImage Man page Source code
IsGlobal.default Man page Source code
IsMatrixEmpty Source code
IsSCT Source code
JS Man page Source code
JS.DimReduc Man page Source code
JS.JackStrawData Man page Source code
JS<- Man page
JS<-.DimReduc Man page
JS<-.JackStrawData Man page
JackRandom Source code
JackStraw Man page Source code
JackStrawData Man page
JackStrawData-class Man page
JackStrawPlot Man page Source code
Key Man page Source code
Key.Assay Man page Source code
Key.DimReduc Man page Source code
Key.Seurat Man page Source code
Key.SpatialImage Man page Source code
Key<- Man page
Key<-.Assay Man page
Key<-.DimReduc Man page
Key<-.SpatialImage Man page
L2CCA Man page Source code
L2Dim Man page Source code
L2Norm Source code Source code
LRDETest Source code
LabelClusters Man page Source code
LabelPoints Man page Source code
Labeler Man page
LengthCheck Source code
LinkedDimPlot Man page Source code
LinkedFeaturePlot Man page Source code
LinkedPlot Man page
LinkedPlots Man page
Load10X_Spatial Man page Source code
LoadAnnoyIndex Man page Source code
LoadSTARmap Man page Source code
Loadings Man page Source code
Loadings.DimReduc Man page Source code
Loadings.Seurat Man page Source code
Loadings<- Man page
Loadings<-.DimReduc Man page
LocalMaxima Source code
LocalStruct Man page Source code
LogNorm Source code
LogNormalize Man page Source code
LogSeuratCommand Man page Source code
LogVMR Man page Source code
Luminance Man page Source code
MASTDETest Source code
MULTIseqDemux Man page Source code
MakeLabels Source code
MapQuery Source code
MapVals Source code
MarkerTest Source code
MatrixRowShuffle Source code
MaxN Source code
MeanRange Source code
MeanVarPlot Man page
Melt Source code
MergeNode Source code
MergeSeurat Man page
MetaFeature Man page Source code
MinMax Man page Source code
Misc Man page Source code
Misc.Assay Man page Source code
Misc.DimReduc Man page Source code
Misc.Seurat Man page Source code
Misc<- Man page
Misc<-.Assay Man page
Misc<-.DimReduc Man page
Misc<-.Seurat Man page
MixingMetric Man page Source code
MultiExIPlot Source code
NBModelComparison Source code
NBResiduals Source code
NNHelper Source code
NNtoMatrix Source code
Neighbor Man page
Neighbor-class Man page
Neighbors Man page Source code
NoAxes Man page Source code
NoGrid Man page Source code
NoLegend Man page Source code
NodeHasChild Source code
NodeHasOnlyChildren Source code
NormalizeData Man page Source code
NormalizeData.Assay Man page Source code
NormalizeData.Seurat Man page Source code
NormalizeData.default Man page Source code
NullImage Source code
OldParamHints Source code
OldWhichCells Man page Source code
OldWhichCells.Assay Man page Source code
OldWhichCells.Seurat Man page Source code
PCAPlot Man page Source code
PCASigGenes Man page Source code
PCHeatmap Man page Source code
PackageCheck Source code
PairwiseIntegrateReference Source code
Parenting Source code
ParseMergePair Source code
ParseRow Source code
PercentAbove Source code
PercentageFeatureSet Man page Source code
PlotBuild Source code
PlotClusterTree Man page Source code
PointLocator Source code
PolyDimPlot Man page Source code
PolyFeaturePlot Man page Source code
PrepDR Source code
PrepSCTIntegration Man page Source code
Project Man page Source code
Project.Seurat Man page Source code
Project<- Man page
Project<-.Seurat Man page
ProjectCellEmbeddings Source code
ProjectDim Man page Source code
Projected Source code
PurpleAndYellow Man page Source code
QuantileSegments Source code
Radius Man page Source code
Radius.STARmap Man page Source code
Radius.SlideSeq Man page Source code
Radius.SpatialImage Man page Source code
Radius.VisiumV1 Man page Source code
RandomName Source code
Read10X Man page Source code
Read10X_Image Man page Source code
Read10X_h5 Man page Source code
ReadAlevin Man page Source code
ReadAlevinCsv Man page Source code
ReadH5AD Man page Source code
ReadH5AD.H5File Man page Source code
ReadH5AD.character Man page Source code
ReadSlideSeq Man page Source code
Reductions Man page Source code
ReferenceRange Source code
RegressOutMatrix Source code
RegroupIdents Man page Source code
RegularizedTheta Source code
RelativeCounts Man page Source code
RenameAssays Man page Source code
RenameCells Man page Source code
RenameCells.Assay Man page Source code
RenameCells.DimReduc Man page Source code
RenameCells.Neighbor Man page Source code
RenameCells.STARmap Source code
RenameCells.Seurat Man page Source code
RenameCells.SlideSeq Source code
RenameCells.SpatialImage Man page Source code
RenameCells.VisiumV1 Man page Source code
RenameIdent Man page
RenameIdents Man page Source code
RenameIdents.Seurat Man page Source code
ReorderIdent Man page Source code
ReorderIdent.Seurat Man page Source code
ReplaceColsC Source code
RestoreLegend Man page Source code
RidgePlot Man page Source code
RotatedAxis Man page Source code
RowMergeMatrices Source code
RowMergeMatricesList Source code
RowMergeSparseMatrices Man page Source code
RowVar Source code
RunALRA Man page Source code
RunALRA.Seurat Man page Source code
RunALRA.default Man page Source code
RunCCA Man page Source code
RunCCA.Seurat Man page Source code
RunCCA.default Man page Source code
RunICA Man page Source code
RunICA.Assay Man page Source code
RunICA.Seurat Man page Source code
RunICA.default Man page Source code
RunIntegration Source code
RunLSI Man page Source code
RunLSI.Assay Man page Source code
RunLSI.Seurat Man page Source code
RunLSI.default Man page Source code
RunLeiden Source code
RunMarkVario Man page Source code
RunModularityClustering Source code
RunModularityClusteringCpp Source code
RunMoransI Man page Source code
RunPCA Man page Source code
RunPCA.Assay Man page Source code
RunPCA.Seurat Man page Source code
RunPCA.default Man page Source code
RunTSNE Man page Source code
RunTSNE.DimReduc Man page Source code
RunTSNE.Seurat Man page Source code
RunTSNE.dist Man page Source code
RunTSNE.matrix Man page Source code
RunUMAP Man page Source code
RunUMAP.Graph Man page Source code
RunUMAP.Seurat Man page Source code
RunUMAP.default Man page Source code
RunUMISampling Source code
RunUMISamplingPerCell Source code
SCTransform Man page Source code
STARmap Man page
STARmap-class Man page
SVFInfo Man page Source code
SVFInfo.Assay Man page Source code
SVFInfo.Seurat Man page Source code
Same Source code
SampleUMI Man page Source code
SaveAnnoyIndex Man page Source code
ScaleColumn Source code
ScaleData Man page Source code
ScaleData.Assay Man page Source code
ScaleData.Seurat Man page Source code
ScaleData.default Man page Source code
ScaleFactors Man page Source code
ScaleFactors.VisiumV1 Man page Source code
ScoreAnchors Source code
ScoreJackStraw Man page Source code
ScoreJackStraw.DimReduc Man page Source code
ScoreJackStraw.JackStrawData Man page Source code
ScoreJackStraw.Seurat Man page Source code
SelectIntegrationFeatures Man page Source code
SetAssayData Man page Source code
SetAssayData.Assay Man page Source code
SetAssayData.Seurat Man page Source code
SetDimReduction Man page
SetHighlight Source code
SetIdent Man page Source code
SetIdent.Seurat Man page Source code
SetIntegrationData Man page Source code
SetQuantile Source code
Seurat Man page
Seurat-class Man page
Seurat-package Man page
SeuratAccess Man page
SeuratAxes Man page Source code
SeuratCommand Man page
SeuratCommand-class Man page
SeuratTheme Man page Source code
ShinyBrush Source code
SingleCorPlot Source code
SingleDimPlot Source code
SingleExIPlot Source code
SingleImageMap Source code
SinglePolyPlot Source code
SingleRasterMap Source code
SingleSpatialPlot Source code
SlideSeq Man page
SlideSeq-class Man page
SparseRowVar Source code
SparseRowVar2 Source code
SparseRowVarStd Source code
SpatialDimPlot Man page Source code
SpatialFeaturePlot Man page Source code
SpatialImage Man page
SpatialImage-class Man page
SpatialPlot Man page Source code
SpatialTheme Man page Source code
SpatiallyVariableFeatures Man page Source code
SpatiallyVariableFeatures.Assay Man page Source code
SpatiallyVariableFeatures.Seurat Man page Source code
SpecificDimPlot Source code
SplitDotPlotGG Man page
SplitObject Man page Source code
Standardize Source code
StashIdent Man page Source code
StashIdent.Seurat Man page Source code
Stdev Man page Source code
Stdev.DimReduc Man page Source code
Stdev.Seurat Man page Source code
StopCellbrowser Man page Source code
SubsetByBarcodeInflections Man page Source code
SubsetData Man page Source code
SubsetData.Assay Man page Source code
SubsetData.Seurat Man page Source code
SubsetVST Source code
Sweep Source code
SysExec Source code
TF.IDF Man page Source code
TSNEPlot Man page Source code
ToNumeric Source code
Tool Man page Source code
Tool.Seurat Man page Source code
Tool<- Man page
Tool<-.Seurat Man page
Tools Man page
Top Source code
TopCells Man page Source code
TopDimFeatures Source code
TopFeatures Man page Source code
TopNeighbors Man page Source code
TransferData Man page Source code
Transform Source code
TransformDataMatrix Source code
UMAPPlot Man page Source code
UpdateAssay Source code
UpdateDimReduction Source code
UpdateJackstraw Source code
UpdateKey Source code
UpdateSeuratObject Man page Source code
UpdateSlots Source code
UpdateSymbolList Man page Source code
ValidateDataForMerge Source code
VariableFeaturePlot Man page Source code
VariableFeatures Man page Source code
VariableFeatures.Assay Man page Source code
VariableFeatures.Seurat Man page Source code
VariableFeatures<- Man page
VariableFeatures<-.Assay Man page
VariableFeatures<-.Seurat Man page
VariableGenePlot Man page
VisiumV1 Man page
VisiumV1-class Man page
VizDimLoadings Man page Source code
VlnPlot Man page Source code
WhichCells Man page Source code
WhichCells.Assay Man page Source code
WhichCells.Seurat Man page Source code
WhiteBackground Man page Source code
WilcoxDETest Source code
WriteEdgeFile Source code
WriteH5AD Man page Source code
WriteH5AD.Seurat Man page Source code
[.Seurat Man page
[.SpatialImage Man page
[[<-,Assay-method Man page
[[<-,Seurat-method Man page
`%iff%` Source code
`%||%` Source code
as.CellDataSet Man page Source code
as.CellDataSet.Seurat Man page Source code
as.Graph Man page Source code
as.Graph.Matrix Man page Source code
as.Graph.Neighbor Man page Source code
as.Graph.matrix Man page Source code
as.Neighbor Man page Source code
as.Neighbor.Graph Man page Source code
as.Seurat Man page Source code
as.Seurat.CellDataSet Man page Source code
as.Seurat.SingleCellExperiment Man page Source code
as.Seurat.loom Man page Source code
as.SingleCellExperiment Man page Source code
as.SingleCellExperiment.Seurat Man page Source code
as.data.frame.Matrix Man page Source code
as.list.SeuratCommand Man page Source code
as.logical.JackStrawData Source code
as.loom Man page Source code
as.loom.Seurat Man page Source code
as.sparse Man page Source code
as.sparse.H5Group Man page Source code
as.sparse.Matrix Man page Source code
as.sparse.data.frame Man page Source code
as.sparse.matrix Man page Source code
bimodLikData Source code
cc.genes Man page
cc.genes.updated.2019 Man page
contrast-theory Man page
dim.Assay Source code
dim.DimReduc Source code
dim.Neighbor Source code
dim.STARmap Source code
dim.Seurat Source code
dim.SlideSeq Source code
dim.SpatialImage Man page Source code
dim.VisiumV1 Source code
dimnames.Assay Source code
dimnames.DimReduc Source code
dimnames.Seurat Source code
droplevels.Seurat Source code
fftRtsne Source code
geom_spatial Source code
geom_spatial_interactive Source code
geom_split_violin Source code
is.null.externalptr Source code
length.DimReduc Source code
levels.Seurat Man page Source code
levels<-.Seurat Man page
merge Man page
merge.Assay Man page Source code
merge.Seurat Man page Source code
names.DimReduc Source code
names.Seurat Source code
pbmc_small Man page
print Man page
print.DimReduc Man page Source code
scalefactors Man page Source code
seurat Man page
seurat-class Man page
subset Man page
subset.Assay Source code
subset.DimReduc Source code
subset.STARmap Source code
subset.Seurat Man page Source code
subset.SlideSeq Source code
subset.SpatialImage Man page Source code
subset.VisiumV1 Source code
Seurat documentation built on Jan. 13, 2021, 7:11 p.m.