API for Seurat
Tools for Single Cell Genomics

Global functions
.AddMetaData Source code
.onAttach Source code
.onLoad Source code
AUCMarkerTest Source code
AddAzimuthResults Man page Source code
AddAzimuthScores Man page Source code
AddDatasetID Source code
AddMetaData Man page
AddModuleScore Man page Source code
AdjustSampleTree Source code
AggregateExpression Man page Source code
AnchorSet Man page
AnchorSet-class Man page
AnnotateAnchors Man page Source code
AnnotateAnchors.IntegrationAnchorSet Man page Source code
AnnotateAnchors.TransferAnchorSet Man page Source code
AnnotateAnchors.default Man page Source code
AnnoyBuildIndex Source code
AnnoyNN Source code
AnnoySearch Source code
Assay-class Man page
Assays Man page
AttachDeps Source code
AugmentPlot Man page Source code
AutoPointSize Man page 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
CalcPerturbSig Man page 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
Cells.SCTModel Man page Source code
Cells.STARmap Man page Source code
Cells.SlideSeq Man page Source code
Cells.VisiumV1 Man page Source code
CellsByIdentities Man page
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
ComputeRMetric Source code
ComputeSNN Source code
ComputeSNNwidth Source code
ConstructNNMat Source code
CountAnchors Source code
CreateAnn Source code Source code
CreateAssayObject Man page
CreateDimReducObject Man page
CreateDummyAssay Source code
CreateSCTAssayObject Man page Source code
CreateSeuratObject Man page
CustomDistance Man page Source code
CustomNormalize Source code
CustomPalette Man page Source code
DESeq2DETest Source code
DEenrichRPlot Man page Source code
DEmethods_checkdots Source code
DEmethods_counts Source code
DEmethods_latent Source code
DEmethods_nocorrect Source code
DEmethods_noprefilter Source code
DFT Source code
DarkTheme Man page Source code
DefaultAssay Man page
DefaultAssay<- Man page
DefaultImage Source code
DefineNormalMixscape 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-class Man page
DirectSNNToFile Source code
DiscretePalette Man page Source code
Distances Man page
DoHeatmap Man page Source code
DotPlot Man page Source code
ElbowPlot Man page Source code
Embeddings Man page
EmpiricalP Source code
ExIPlot Source code
ExpMean Man page Source code
ExpSD Man page Source code
ExpVar 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
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.Assay Man page Source code
FindMarkers.DimReduc Man page Source code
FindMarkers.SCTAssay Man page Source code
FindMarkers.Seurat Man page Source code
FindMarkers.default Man page Source code
FindMarkersNode Man page
FindModalityWeights Source code
FindMultiModalNeighbors Man page Source code
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
FindSubCluster Man page Source code
FindThresh Source code
FindTransferAnchors Man page Source code
FindVariableFeatures Man page Source code
FindVariableFeatures.Assay Man page Source code
FindVariableFeatures.SCTAssay 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
FoldChange Man page Source code
FoldChange.Assay Man page Source code
FoldChange.DimReduc Man page Source code
FoldChange.Seurat Man page Source code
FoldChange.default Man page 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
GetCellOffsets Source code
GetDescendants Source code
GetFeatureGroups Source code
GetImage Man page
GetImage.STARmap Man page Source code
GetImage.SlideSeq Man page Source code
GetImage.VisiumV1 Man page Source code
GetIntegrationData Man page Source code
GetLeftDescendants Source code
GetMissingPerturb Source code
GetResidual Man page Source code
GetResidualSCTModel Source code
GetRightDescendants Source code
GetTissueCoordinates Man page
GetTissueCoordinates.STARmap Man page Source code
GetTissueCoordinates.SlideSeq Man page Source code
GetTissueCoordinates.VisiumV1 Man page Source code
GetTransferPredictions Man page Source code
GetXYAesthetics Source code
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
HVFInfo.SCTAssay 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
Idents<- Man page
IdentsToCells Source code
Images Man page
Index Man page
Index<- Man page
Indices Man page
IntegrateData Man page Source code
IntegrateDataC Source code
IntegrateEmbeddings Man page Source code
IntegrateEmbeddings.IntegrationAnchorSet Man page Source code
IntegrateEmbeddings.TransferAnchorSet Man page Source code
IntegrationAnchorSet Man page
IntegrationAnchorSet-class Man page
IntegrationData Man page
IntegrationData-class Man page
Intensity Man page Source code
Interleave Source code
InvertCoordinate Source code
InvertHex Source code
IsGlobal Man page
IsMatrixEmpty Source code
IsSCT Source code
IsVSTout Source code
JS Man page
JS<- Man page
JackRandom Source code
JackStraw Man page Source code
JackStrawData-class Man page
JackStrawPlot Man page Source code
Key Man page
Key<- 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
Loadings<- Man page
LocalMaxima Source code
LocalStruct Man page Source code
LogNorm Source code
LogNormalize Man page Source code
LogSeuratCommand Man page
LogVMR Man page Source code
Luminance Man page Source code
MASTDETest Source code
MULTIseqDemux Man page Source code
MakeLabels Source code
MapQuery Man page Source code
MapQueryData Source code
MapVals Source code
MappingScore Man page Source code
MappingScore.AnchorSet Man page Source code
MappingScore.default Man page Source code
MarkerTest Source code
MatrixRowShuffle Source code
MaxN Source code
MeanRange Source code
MeanVarPlot Man page
Melt Source code
MergeNode Source code
MetaFeature Man page Source code
MinMax Man page Source code
Misc Man page
Misc<- Man page
MixingMetric Man page Source code
MixscapeHeatmap Man page Source code
MixscapeLDA Man page Source code
ModalityWeights Man page
ModalityWeights-class Man page
ModifyParam Source code
MultiExIPlot Source code
MultiModalNN Source code
NBModelComparison Source code
NBResiduals Source code
NNHelper Source code
NNPlot Man page Source code
NNdist Source code
NNtoMatrix Source code
Neighbor-class Man page
Neighbors Man page
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
Online Source code
PCAPlot Man page Source code
PCASigGenes Man page Source code
PCHeatmap Man page Source code
PairwiseIntegrateReference Source code
Parenting Source code
ParseMergePair Source code
ParseRow Source code
PercentAbove Man page Source code
PercentageFeatureSet Man page Source code
PerformDE Source code
PerturbDiff Source code
PlotBuild Source code
PlotClusterTree Man page Source code
PlotPerturbScore Man page Source code
PointLocator Source code
PolyDimPlot Man page Source code
PolyFeaturePlot Man page Source code
PredictAssay Man page Source code
PrepDR Source code
PrepLDA Man page Source code
PrepSCTFindMarkers Man page Source code
PrepSCTIntegration Man page Source code
PrepVSTResults Source code
Project Man page
Project<- Man page
ProjectCellEmbeddings Source code
ProjectDim Man page Source code
ProjectSVD Source code
ProjectUMAP Man page Source code
ProjectUMAP.DimReduc Man page Source code
ProjectUMAP.Seurat Man page Source code
ProjectUMAP.default Man page Source code
ProjectVec Source code
Projected Source code
PseudobulkExpression Source code
PurpleAndYellow Man page Source code
QuantileSegments Source code
Radius Man page
Radius.STARmap Man page Source code
Radius.SlideSeq Man page Source code
Radius.VisiumV1 Man page Source code
RandomName Source code
ReLu Source code
Read10X Man page Source code
Read10X_Image Man page Source code
Read10X_h5 Man page Source code
ReadMtx Man page Source code
ReadParseBio Man page Source code
ReadSTARsolo Man page Source code
ReadSlideSeq Man page Source code
ReciprocalProject Source code
Reductions Man page
ReferenceRange Source code
RegressOutMatrix Source code
RegroupIdents Man page Source code
RegularizedTheta Source code
RelativeCounts Man page Source code
RemoveLastField Source code
RenameCells Man page
RenameCells.SCTAssay Man page Source code
RenameCells.STARmap Man page Source code
RenameCells.SlideSeq Man page Source code
RenameCells.VisiumV1 Man page Source code
RenameIdents Man page
ReorderIdent Man page
ReplaceColsC Source code
RescaleQuery Source code
RestoreLegend Man page Source code
RidgePlot Man page Source code
RotatedAxis Man page Source code
RowMeanSparse Source code
RowMergeMatrices Source code
RowMergeSparseMatrices Man page
RowSparseCheck Source code
RowSumSparse Source code
RowVar Source code
RowVarSparse 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
RunLDA Man page Source code
RunLDA.Assay Man page Source code
RunLDA.Seurat Man page Source code
RunLDA.default Man page Source code
RunLeiden Source code
RunMarkVario Man page Source code
RunMixscape 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
RunSLSI Man page Source code
RunSLSI.Assay Man page Source code
RunSLSI.Seurat Man page Source code
RunSLSI.default Man page Source code
RunSPCA Man page Source code
RunSPCA.Assay Man page Source code
RunSPCA.Seurat Man page Source code
RunSPCA.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.Neighbor Man page Source code
RunUMAP.Seurat Man page Source code
RunUMAP.default Man page Source code
RunUMISampling Source code
RunUMISamplingPerCell Source code
SCTAssay Man page
SCTAssay-class Man page
SCTModel Man page
SCTModel_to_vst Source code
SCTResults Man page Source code
SCTResults.SCTAssay Man page Source code
SCTResults.SCTModel Man page Source code
SCTResults.Seurat Man page Source code
SCTResults<- Man page
SCTResults<-.SCTAssay Man page
SCTResults<-.SCTModel Man page
SCTransform Man page Source code
SNN_SmallestNonzero_Dist Source code
STARmap Man page
STARmap-class Man page
SVFInfo Man page
SampleIntegrationOrder 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 Source code
ScoreAnchors Source code
ScoreHelper 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
SetHighlight Source code
SetIdent Man page
SetIntegrationData Man page Source code
SetQuantile Man page Source code
Seurat Man page
Seurat-class Man page
Seurat-package Man page
SeuratAxes Man page Source code
SeuratCommand-class Man page
SeuratTheme Man page Source code
ShinyBrush Source code
SingleCorPlot Man page Source code
SingleDimPlot Man page Source code
SingleExIPlot Man page Source code
SingleImageMap Man page Source code
SinglePolyPlot Source code
SingleRasterMap Man page Source code
SingleSpatialPlot Man page 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-class Man page
SpatialPlot Man page Source code
SpatialTheme Man page Source code
SpatiallyVariableFeatures Man page
SpecificDimPlot Source code
SplitDotPlotGG Man page
SplitObject Man page Source code
Standardize Source code
StashIdent Man page
Stdev Man page
SubsetByBarcodeInflections Man page Source code
SubsetVST Source code
Sweep Source code
SysExec Source code
TSNEPlot Man page Source code
ToNumeric Source code
Tool Man page
Tool<- Man page
Top Source code
TopCells Man page Source code
TopDEGenesMixscape Source code
TopDimFeatures Source code
TopFeatures Man page Source code
TopNeighbors Man page Source code
TransferAnchorSet Man page
TransferAnchorSet-class Man page
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
UpdateSCTAssays Man page Source code
UpdateSeuratObject Man page
UpdateSlots Source code
UpdateSymbolList Man page Source code
ValidateCellGroups Source code
ValidateDataForMerge Source code
ValidateParams_FindTransferAnchors Source code
ValidateParams_IntegrateEmbeddings_IntegrationAnchors Source code
ValidateParams_IntegrateEmbeddings_TransferAnchors Source code
ValidateParams_TransferData Source code
VariableFeaturePlot Man page Source code
VariableFeatures Man page
VariableFeatures<- 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
WhiteBackground Man page Source code
WilcoxDETest Source code
WriteEdgeFile Source code
`%iff%` Source code
`%||%` Source code
as.CellDataSet Man page Source code
as.CellDataSet.Seurat Man page Source code
as.Graph Man page
as.Neighbor Man page
as.Seurat Man page
as.Seurat.CellDataSet Man page Source code
as.Seurat.SingleCellExperiment 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.sparse Man page
as.sparse.H5Group Man page Source code
bimodLikData Source code
cc.genes Man page
cc.genes.updated.2019 Man page
contrast-theory Man page
dim.STARmap Source code
dim.SlideSeq Source code
dim.VisiumV1 Source code
fast_dist Source code
fftRtsne Source code
geom_spatial Source code
geom_spatial_interactive Source code
geom_split_violin Source code
impute_dist Source code
is.null.externalptr Source code
levels.SCTAssay Man page Source code
levels<-.SCTAssay Man page
merge.SCTAssay Man page Source code
reexports Man page
row_mean_dgcmatrix Source code
row_sum_dgcmatrix Source code
row_var_dgcmatrix Source code
scalefactors Man page Source code
subset.AnchorSet Man page Source code
subset.SCTAssay Source code
subset.STARmap Source code
subset.SlideSeq Source code
subset.VisiumV1 Source code
Seurat documentation built on Jan. 15, 2022, 1:07 a.m.