API for lambdamoses/SeuratBasics
Slimmed down version of Seurat
| Global functions | |
|---|---|
| .AddMetaData | Source code |
| .onLoad | Source code |
| AUCMarkerTest | 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 |
| 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 |
| Bandwidth | Source code |
| BarcodeInflectionsPlot | Man page 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 |
| 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.default | Man page Source code |
| CellsByIdentities | 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 |
| CombinePlots | Man page Source code |
| Command | Man page Source code |
| Command.Seurat | Man page Source code |
| ComputeSNN | Source code |
| CreateAssayObject | Man page Source code |
| CreateDimReducObject | Man page Source code |
| CreateSeuratObject | Man page Source code |
| CustomDistance | Man page Source code |
| CustomNormalize | Source code |
| CustomPalette | Man page Source code |
| DESeq2DETest | 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<- | Man page |
| DefaultAssay<-.Seurat | Man page |
| DefaultDimReduc | 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 |
| 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 |
| 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 | 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 |
| FilterObjects | Source code |
| FindAllMarkers | Man page Source code |
| FindClusters | Man page Source code |
| FindClusters.Seurat | Man page Source code |
| FindClusters.default | Man page Source code |
| FindMarkers | Man page Source code |
| FindMarkers.Seurat | Man page Source code |
| FindMarkers.default | Man page Source code |
| FindMarkersNode | Man page |
| 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 |
| FindThresh | 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 |
| FontSize | Man page Source code |
| GGpointToBase | Source code |
| GLMDETest | Source code |
| GenePlot | Man page |
| 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 |
| GetResidual | Man page Source code |
| GetResidualVstOut | Source code |
| GetXYAesthetics | Source code |
| Graph | Man page |
| Graph-class | Man page |
| 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 |
| Idents | Man page Source code |
| Idents.Seurat | Man page Source code |
| Idents<- | Man page |
| Idents<-.Seurat | Man page |
| Interleave | Source code |
| InvertHex | Source code |
| IsGlobal | Man page Source code |
| IsGlobal.DimReduc | 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<- | Man page |
| Key<-.Assay | Man page |
| Key<-.DimReduc | Man page |
| L2Norm | Source code Source code |
| LRDETest | Source code |
| LabelClusters | Man page Source code |
| LabelPoints | Man page Source code |
| Labeler | Man page |
| LengthCheck | 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 |
| LogNorm | Source code |
| LogNormalize | Man page Source code |
| LogSeuratCommand | Man page Source code |
| LogVMR | Man page Source code |
| MASTDETest | Source code |
| MULTIseqDemux | Man page Source code |
| MakeLabels | Source code |
| MapVals | Source code |
| MarkerTest | Source code |
| MatrixRowShuffle | Source code |
| MaxN | Source code |
| MeanVarPlot | Man page |
| Melt | 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.Seurat | Man page Source code |
| Misc<- | Man page |
| Misc<-.Assay | Man page |
| Misc<-.Seurat | Man page |
| NBModelComparison | Source code |
| NBResiduals | Source code |
| NNHelper | Source code |
| NoAxes | Man page Source code |
| NoGrid | Man page Source code |
| NoLegend | Man page 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 |
| 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 |
| Parenting | Source code |
| PercentAbove | Source code |
| PercentageFeatureSet | Man page Source code |
| PlotBuild | Source code |
| PointLocator | Source code |
| PolyDimPlot | Man page Source code |
| PolyFeaturePlot | Man page Source code |
| PrepDR | Source code |
| Project | Man page Source code |
| Project.Seurat | Man page Source code |
| Project<- | Man page |
| Project<-.Seurat | Man page |
| ProjectDim | Man page Source code |
| Projected | Source code |
| PurpleAndYellow | Man page Source code |
| QuantileSegments | Source code |
| RandomName | Source code |
| Read10X | 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 |
| Reductions | Man page 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.Seurat | 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 |
| RowMergeSparseMatrices | Man page Source code |
| RowVar | Source code |
| RunLeiden | Source code |
| RunModularityClustering | Source code |
| RunModularityClusteringCpp | 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.Seurat | Man page Source code |
| RunUMAP.default | Man page Source code |
| RunUMISampling | Source code |
| RunUMISamplingPerCell | Source code |
| SCTransform | Man page Source code |
| Same | Source code |
| SampleUMI | 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 |
| ScoreJackStraw | Man page Source code |
| ScoreJackStraw.DimReduc | Man page Source code |
| ScoreJackStraw.JackStrawData | Man page Source code |
| ScoreJackStraw.Seurat | 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 |
| SetQuantile | Source code |
| Seurat | Man page |
| Seurat-class | Man page |
| SeuratAccess | Man page |
| SeuratAxes | Man page Source code |
| SeuratBasics-package | Man page |
| SeuratCommand | Man page |
| SeuratCommand-class | Man page |
| SeuratTheme | Man page Source code |
| SingleCorPlot | Source code |
| SingleDimPlot | Source code |
| SingleExIPlot | Source code |
| SingleImageMap | Source code |
| SinglePolyPlot | Source code |
| SingleRasterMap | Source code |
| SparseRowVar | Source code |
| SparseRowVar2 | Source code |
| SparseRowVarStd | Source code |
| SpatialTheme | 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 |
| SubsetByBarcodeInflections | Man page Source code |
| SubsetData | Man page Source code |
| SubsetData.Assay | Man page Source code |
| SubsetData.Seurat | Man page Source code |
| Sweep | Source code |
| SysExec | 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 |
| TopFeatures | Man page Source code |
| UMAPPlot | Man page Source code |
| UpdateAssay | Source code |
| UpdateKey | Source code |
| UpdateSlots | 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 |
| 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 |
| [[<-,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.matrix | 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 |
| dim.Assay | Source code |
| dim.DimReduc | Source code |
| dim.Seurat | Source code |
| dimnames.Assay | Source code |
| dimnames.DimReduc | Source code |
| dimnames.Seurat | Source code |
| droplevels.Seurat | Source code |
| fftRtsne | Source code |
| geom_split_violin | 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 |
| Man page | |
| print.DimReduc | Man page Source code |
| seurat | Man page |
| seurat-class | Man page |
| subset | Man page |
| subset.Assay | Source code |
| subset.DimReduc | Source code |
| subset.Seurat | Man page Source code |
