API for ibseq/scs-analysis
Tools for Single Cell Genomics
| Global functions | |
|---|---|
| .AddMetaData | Source code |
| .onAttach | Source code |
| .onLoad | Source code |
| AUCMarkerTest | 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 | 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 |
| DefaultDimReduc | Source code |
| 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.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 |
| 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 |
| 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 |
| 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 |
| PrepSCTIntegration | Man page Source code |
| PrepVSTResults | Source code |
| Project | Man page |
| Project<- | Man page |
| ProjectCellEmbeddings | Source code |
| ProjectDim | Man page 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 |
| ReadSlideSeq | Man page 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 |
| RowMergeMatrices | Source code |
| RowMergeSparseMatrices | Man page |
| RowVar | 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 |
| 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 | 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 | 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-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 |
| 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 |
