| %iff% |
Man page
|
| %||% |
Man page
|
| .Abbrv |
Source code
|
| .AddMetaData |
Source code
|
| .AsList |
Source code
|
| .BoundariesByImage |
Source code
|
| .CalcN.IterableMatrix |
Source code
|
| .Cut |
Source code
|
| .FeatureRank |
Source code
|
| .FeatureVar |
Source code
|
| .FindE |
Source code
|
| .Mean |
Source code
|
| .MolsByFOV |
Source code
|
| .ReadVitessceClusters |
Source code
|
| .ReadVitessceGenes |
Source code
|
| .SparseFeatureVar |
Source code
|
| .SparseMean |
Source code
|
| .SparseNormalize |
Source code
|
| .VST |
Source code
|
| .onAttach |
Source code
|
| .onLoad |
Source code
|
| .rd_methods |
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
|
| BridgeCellsRepresentation |
Man page
Source code
|
| BridgeReferenceSet |
Man page
|
| BridgeReferenceSet-class |
Man page
|
| BuildClusterTree |
Man page
Source code
|
| BuildNicheAssay |
Man page
Source code
|
| BuildSampleTree |
Source code
|
| CCAIntegration |
Man page
Source code
|
| CalcDispersion |
Man page
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.SCTAssay |
Source code
|
| 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
|
| CheckMetaVarName |
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
|
| CountSketch |
Man page
Source code
|
| CreateAnn |
Source code
Source code
|
| CreateAssayObject |
Man page
|
| CreateCategoryMatrix |
Man page
Source code
|
| CreateDimReducObject |
Man page
|
| CreateDummyAssay |
Source code
|
| CreateIntegrationGroups |
Source code
|
| CreateSCTAssay |
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
|
| DISP |
Man page
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
|
| FastRPCAIntegration |
Man page
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
|
| FeatureSketch |
Source code
|
| Features.SCTAssay |
Source code
|
| Features.SCTModel |
Source code
|
| FetchData |
Man page
|
| FetchData.VisiumV1 |
Source code
|
| FetchResidualSCTModel |
Man page
Source code
|
| FetchResiduals |
Man page
Source code
|
| FetchResiduals_reference |
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
|
| FindAnchors_v3 |
Source code
|
| FindAnchors_v5 |
Source code
|
| FindAssayAnchor |
Source code
|
| FindBridgeAnchor |
Man page
Source code
|
| FindBridgeIntegrationAnchors |
Man page
Source code
|
| FindBridgeTransferAnchors |
Man page
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.StdAssay |
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.StdAssay |
Source code
|
| FindVariableFeatures.V3Matrix |
Man page
Source code
|
| FindVariableFeatures.default |
Source code
|
| FindVariableGenes |
Man page
|
| FindWeights |
Source code
|
| FindWeightsC |
Source code
|
| FindWeightsNN |
Source code
|
| FoldChange |
Man page
Source code
|
| FoldChange.Assay |
Man page
Source code
|
| FoldChange.DimReduc |
Man page
Source code
|
| FoldChange.SCTAssay |
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
|
| GaussianSketch |
Man page
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
|
| GetResidualsChunked |
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
|
| HarmonyIntegration |
Man page
Source code
|
| HnswNN |
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
|
| ImageDimPlot |
Man page
Source code
|
| ImageFeaturePlot |
Man page
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
|
| IntegrateLayers |
Man page
Source code
|
| IntegrationAnchorSet |
Man page
|
| IntegrationAnchorSet-class |
Man page
|
| IntegrationData |
Man page
|
| IntegrationData-class |
Man page
|
| IntegrationReferenceIndex |
Source code
|
| 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
|
| JLEmbed |
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
|
| JointPCAIntegration |
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
|
| LeverageScore |
Man page
Source code
|
| LeverageScore.Assay |
Man page
|
| LeverageScore.Seurat |
Man page
Source code
|
| LeverageScore.StdAssay |
Man page
Source code
|
| LeverageScore.default |
Man page
Source code
|
| LinkedDimPlot |
Man page
Source code
|
| LinkedFeaturePlot |
Man page
Source code
|
| LinkedPlot |
Man page
|
| LinkedPlots |
Man page
|
| Load10X_Spatial |
Man page
Source code
|
| LoadAkoya |
Man page
Source code
|
| LoadAnnoyIndex |
Man page
Source code
|
| LoadCurioSeeker |
Man page
Source code
|
| LoadHuBMAPCODEX |
Man page
Source code
|
| LoadNanostring |
Man page
Source code
|
| LoadSTARmap |
Man page
Source code
|
| LoadVizgen |
Man page
Source code
|
| LoadXenium |
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
|
| LogNormalize.IterableMatrix |
Source code
|
| LogNormalize.V3Matrix |
Man page
Source code
|
| LogNormalize.data.frame |
Man page
Source code
|
| LogNormalize.default |
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
|
| MVP |
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
|
| MergeSparseMatrices |
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
|
| NNtoGraph |
Man page
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.StdAssay |
Source code
|
| NormalizeData.V3Matrix |
Man page
Source code
|
| NormalizeData.default |
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
|
| PrepDR5 |
Source code
|
| PrepLDA |
Man page
Source code
|
| PrepSCTFindMarkers |
Man page
Source code
|
| PrepSCTFindMarkers.V5 |
Source code
|
| PrepSCTIntegration |
Man page
Source code
|
| PrepVSTResults |
Source code
|
| PrepareBridgeReference |
Man page
|
| Project |
Man page
|
| Project<- |
Man page
|
| ProjectCellEmbeddings |
Man page
Source code
|
| ProjectCellEmbeddings.Assay |
Man page
Source code
|
| ProjectCellEmbeddings.IterableMatrix |
Man page
Source code
|
| ProjectCellEmbeddings.SCTAssay |
Man page
Source code
|
| ProjectCellEmbeddings.Seurat |
Man page
Source code
|
| ProjectCellEmbeddings.StdAssay |
Man page
Source code
|
| ProjectCellEmbeddings.default |
Man page
Source code
|
| ProjectData |
Man page
Source code
|
| ProjectDim |
Man page
Source code
|
| ProjectDimReduc |
Man page
Source code
|
| ProjectIntegration |
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 |
Man page
Source code
|
| PseudobulkExpression.Assay |
Source code
|
| PseudobulkExpression.Seurat |
Source code
|
| PseudobulkExpression.StdAssay |
Source code
|
| PurpleAndYellow |
Man page
Source code
|
| QuantileSegments |
Source code
|
| RPCAIntegration |
Man page
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
|
| Read10X_probe_metadata |
Man page
Source code
|
| ReadAkoya |
Man page
Source code
|
| ReadMtx |
Man page
Source code
|
| ReadNanostring |
Man page
Source code
|
| ReadParseBio |
Man page
Source code
|
| ReadSTARsolo |
Man page
Source code
|
| ReadSlideSeq |
Man page
Source code
|
| ReadVitessce |
Man page
Source code
|
| ReadVizgen |
Man page
Source code
|
| ReadXenium |
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
|
| 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
|
| RunGraphLaplacian |
Man page
Source code
|
| RunGraphLaplacian.Seurat |
Man page
Source code
|
| RunGraphLaplacian.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.Seurat5 |
Source code
|
| RunPCA.StdAssay |
Source code
|
| RunPCA.default |
Man page
Source code
|
| RunPCA_Sparse |
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.Assay5 |
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
|
| SCTransform.Assay |
Man page
Source code
|
| SCTransform.IterableMatrix |
Man page
Source code
|
| SCTransform.Seurat |
Man page
Source code
|
| SCTransform.StdAssay |
Source code
|
| SCTransform.default |
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.IterableMatrix |
Man page
Source code
|
| ScaleData.Seurat |
Man page
Source code
|
| ScaleData.StdAssay |
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
|
| SelectIntegrationFeatures5 |
Man page
Source code
|
| SelectSCTIntegrationFeatures |
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
|
| SingleImagePlot |
Man page
Source code
|
| SinglePolyPlot |
Source code
|
| SingleRasterMap |
Man page
Source code
|
| SingleSpatialPlot |
Man page
Source code
|
| SketchData |
Man page
Source code
|
| SlideSeq |
Man page
|
| SlideSeq-class |
Man page
|
| SmoothLabels |
Source code
|
| SparseMeanSd |
Source code
|
| 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
|
| SweepNonzero |
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
|
| TransferExpressionNN |
Source code
|
| TransferLablesNN |
Source code
|
| TransferSketchLabels |
Man page
Source code
|
| Transform |
Source code
|
| TransformDataMatrix |
Source code
|
| UMAPPlot |
Man page
Source code
|
| UnSketchEmbeddings |
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
|
| VST |
Man page
Source code
|
| VST.IterableMatrix |
Man page
Source code
|
| VST.default |
Man page
Source code
|
| VST.dgCMatrix |
Man page
Source code
|
| VST.matrix |
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.SCTAssay |
Source code
|
| VariableFeatures.SCTModel |
Source code
|
| 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
|
| 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
|
| as.sparse.IterableMatrix |
Source code
|
| bimodLikData |
Source code
|
| build.cellcomp.matrix |
Source code
|
| cc.genes |
Man page
|
| cc.genes.updated.2019 |
Man page
|
| components |
Man page
|
| components.SCTAssay |
Source code
|
| contrast-theory |
Man page
|
| crossprod_BPCells |
Source code
|
| crossprod_DelayedAssay |
Source code
|
| dim.STARmap |
Source code
|
| dim.SlideSeq |
Source code
|
| dim.VisiumV1 |
Source code
|
| fast_dist |
Source code
|
| fftRtsne |
Source code
|
| fortify |
Man page
|
| fortify-Spatial |
Man page
|
| fortify.Centroids |
Man page
Source code
|
| fortify.Molecules |
Man page
Source code
|
| fortify.Segmentation |
Man page
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
|
| writing-integration |
Man page
|
