Man pages for SeuratObject
Data Structures for Single Cell Data
| AddMetaData | Add in metadata associated with either cells or features. |
| AddMetaData-StdAssay | Add in metadata associated with either cells or features. |
| aggregate | Aggregate Molecules into an Expression Matrix |
| angles | Radian/Degree Conversions |
| as.Centroids | Convert Segmentation Layers |
| as.Graph | Coerce to a 'Graph' Object |
| as.list.SeuratCommand | Coerce a 'SeuratCommand' to a list |
| as.matrix.LogMap | Coerce Logical Maps to Matrices |
| as.Neighbor | Coerce to a 'Neighbor' Object |
| as.Seurat | Coerce to a 'Seurat' Object |
| as.sparse | Cast to Sparse |
| Boundaries | Get, Set, and Query Segmentation Boundaries |
| cash-.Assay | Layer Data |
| cash-.Assay5 | Layer Data |
| cash-.Seurat | Cell-Level Meta Data |
| cash-.SeuratCommand | Command Log Parameter Access |
| cash-.StdAssay | Layer Data |
| CastAssay | Cast Assay Layers |
| CastAssay-StdAssay | Cast Assay Layers |
| Cells | Cell and Feature Names |
| CellsByIdentities | Get cell names grouped by identity class |
| CellsByImage | Get a vector of cell names associated with an image (or set... |
| Cells-StdAssay | Cell and Feature Names |
| Centroids-class | The 'Centroids' Class |
| Centroids-methods | 'Centroids' Methods |
| CheckDots | Check the Use of Dots |
| CheckFeaturesNames | Check features names format |
| CheckGC | Conditional Garbage Collection |
| CheckLayersName | Check layers names for the input list |
| CheckMatrix | Check Matrix Validity |
| ClassKey | Generate a Class Key |
| colMeans-Assay-method | Row and Column Sums and Means |
| colMeans-Seurat-method | Row and Column Sums and Means |
| Command | Get SeuratCommands |
| CreateAssay5Object | Create a v5 Assay object |
| CreateAssayObject | Create an Assay object |
| CreateCentroids | Create a 'Centroids' Objects |
| CreateDimReducObject | Create a DimReduc object |
| CreateFOV | Create Spatial Coordinates |
| CreateMolecules | Create a 'Molecules' Object |
| CreateSegmentation | Create a 'Segmentation' Objects |
| CreateSeuratObject | Create a 'Seurat' object |
| Crop | Crop Coordinates |
| DefaultAssay | Default Assay |
| DefaultAssay-StdAssay | Default Assay |
| DefaultDimReduc | Find the default 'DimReduc' |
| DefaultFOV | Get and Set the Default FOV |
| DefaultLayer | Default Layer |
| DefaultLayer-StdAssay | Default Layer |
| dim.Assay | Feature and Cell Numbers |
| dim.Assay5 | Feature and Cell Numbers |
| dim.DimReduc | Dimensional Reduction Meta-Information |
| dimnames.Assay | Assay-Level Feature and Cell Names |
| dimnames.Assay5 | Assay-Level Feature and Cell Names |
| dimnames.Seurat | Feature and Cell Names |
| dimnames.StdAssay | Assay-Level Feature and Cell Names |
| dim.Seurat | Feature and Cell Numbers |
| dim.StdAssay | Feature and Cell Numbers |
| Distances | Get the Neighbor nearest neighbors distance matrix |
| dot-AssayClass | Assay Class Label |
| dot-BPMatrixMode | 'BPCells' Matrix Mode |
| dot-CalcN | Calculate nCount and nFeature |
| dot-CheckFmargin | Check Feature Margin |
| dot-ClassPkg | Get the Package that Defines a Class |
| dot-Collections | Identify Object Collections |
| dot-Contains | Get Parent S4 Classes |
| dot-CreateStdAssay | Generic Assay Creation |
| dot-DefaultFOV | Find the Default FOV |
| dot-Deprecate | Deprecate Functions and Arguments |
| dot-DiskLoad | Disk Loading Function |
| dot-DollarNames.Assay | Dollar-sign Autocompletion |
| dot-DollarNames.Assay5 | Dollar-sign Autocompletion |
| dot-DollarNames.Seurat | Dollar-sign Autocompletion |
| dot-DollarNames.SeuratCommand | Dollar-sign Autocompletion |
| dot-DollarNames.StdAssay | Dollar-sign Autocompletion |
| dot-FileMove | Move Files and Directories |
| dot-FilePath | Find a File Path |
| dot-FilterObjects | Find Subobjects Of A Certain Class |
| dot-FindObject | Find A Subobject |
| dot-GetConsensusFeatures | Returns the most frequently observed features in... |
| dot-GetMethod | Get a Method |
| dot-GetVariableFeatures | Returns the top variable features from a data frame of highly... |
| dot-IsFutureSeurat | Test Future Compatibility with 'Seurat' |
| dot-MARGIN | Get the Margin of an Object |
| dot-PropagateList | Propagate a List |
| dot-RandomKey | Generate a Random Key |
| dot-SparseSlots | Identify Sparse Slots |
| dot-Subobjects | Get the Subobject Names |
| droplevels.LogMap | Drop Unused Logical Map Values |
| Embeddings | Get Cell Embeddings |
| EmptyDF | Empty Data Frames |
| EmptyMatrix | Empty Matrices |
| ExtractField | Extract delimiter information from a string. |
| FetchData | Access cellular data |
| FOV-methods | 'FOV' Methods |
| FOV-validity | FOV Validity |
| GetImage | Get image data |
| GetTissueCoordinates | Get tissue coordinates |
| Graph-class | The Graph Class |
| Idents | Get, set, and manipulate an object's identity classes |
| Images | Pull spatial image names |
| Indices | Get Neighbor nearest neighbor index matrices |
| intersect.LogMap | Find Common Logical Map Values |
| IsGlobal | Is an object global/persistent? |
| IsMatrixEmpty | Check if a matrix is empty |
| IsNamedList | Check List Names |
| IsSparse | Is a Matrix Sparse |
| JackStrawData-class | The JackStrawData Class |
| JackStrawData-methods | 'JackStrawData' Methods |
| JS | Get and set JackStraw information |
| Key | Get and set object keys |
| labels.LogMap | Find Observations by Value |
| Loadings | Get and set feature loadings |
| LogMap-class | A Logical Map |
| LogMap-validity | Logical Map Validity |
| LogSeuratCommand | Log a command |
| MatchCells | Match Cells |
| merge.Assay | Merge Assays |
| merge.Assay5 | Merge Assays |
| merge.DimReduc | Merge Dimensional Reductions |
| merge.Seurat | Merge Seurat Objects |
| merge.StdAssay | Merge Assays |
| Misc | Get and set miscellaneous data |
| Misc-StdAssay | Get and set miscellaneous data |
| Molecules-class | The Spatial Molecules Class |
| Molecules-methods | 'Molecules' Methods |
| names.Seurat | Subobject Names |
| Neighbor-class | The Neighbor class |
| Neighbor-methods | 'Neighbor' Methods |
| NNIndex | Get Neighbor algorithm index |
| ObjectAccess | Query Specific Object Types |
| old-assign | Original double-bracket assign |
| oldseurat-class | The Seurat Class |
| Overlay | Overlay 'Spatial' Objects Over One Another |
| pbmc_small | A small example version of the PBMC dataset |
| PolyVtx | Polygon Vertices |
| print.DimReduc | Print Top Feature Loadings |
| Project | Get and set project information |
| Radius | Get the spot radius from an image |
| RandomName | Generate a random name |
| reexports | Objects exported from other packages |
| RegisterSparseMatrix | Register Sparse Matrix Classes |
| RenameAssays | Rename assays in a 'Seurat' object |
| RenameCells | Rename cells |
| RenameCells-StdAssay | Rename cells |
| RowMergeSparseMatrices | Merge Sparse Matrices by Row |
| s4list | S4/List Conversion |
| Segmentation-class | The 'Segmentation' Class |
| Segmentation-methods | 'Segmentation' Methods |
| Segmentation-validity | Segmentation Validity |
| set-if-na | Set If or If Not 'NA' |
| set-if-null | Set If or If Not 'NULL' |
| Seurat-class | The Seurat Class |
| SeuratCommand-class | The 'SeuratCommand' Class |
| SeuratObject-package | SeuratObject: Data Structures for Single Cell Data |
| Seurat-validity | Seurat Object Validity |
| show-Assay-method | V3 Assay Overview |
| show-DimReduc-method | Dimensional Reduction Overview |
| show-Graph-method | Graph Object Overview |
| show-LogMap-method | 'LogMap' Object Overview |
| show-oldseurat-method | Old Seurat Object Overview |
| show-SeuratCommand-method | Command Log Overview |
| show-Seurat-method | Seurat Object Overview |
| show-StdAssay-method | V5 Assay Overview |
| Simplify | Simplify Geometry |
| SparseEmptyMatrix | Generate empty dgC sparse matrix |
| SpatialImage-methods | 'SpatialImage' methods |
| split.Assay | Split an Assay |
| split.Assay5 | Split an Assay |
| SplitLayers | Split and Join Layers Together |
| split.Seurat | Split an Assay |
| split.StdAssay | Split an Assay |
| Stdev | Get the standard deviations for an object |
| StitchMatrix | Stitch Matrices Together |
| sub-.Assay | Layer Data |
| sub-.Assay5 | Layer Data |
| sub-.DimReduc | Get Feature Loadings |
| sub-LogMap-method | Matrix-like Subsetting for Logical Maps |
| subset.Assay | Subset an Assay |
| subset.Assay5 | Subset an Assay |
| subset.DimReduc | Subset a Dimensional Reduction |
| subset.Seurat | Subset 'Seurat' Objects |
| subset.StdAssay | Subset an Assay |
| sub-.SeuratCommand | Command Log Data Access |
| sub-.StdAssay | Layer Data |
| sub-sub-.Assay | Feature-Level Meta Data |
| sub-sub-.Assay5 | Feature-Level Meta Data |
| sub-sub-.DimReduc | Get Cell Embeddings |
| sub-sub-LogMap-internal-method | 'LogMap' Interaction Methods |
| sub-subset-Seurat | Add Subobjects |
| sub-subset-Seurat-character-missing-StdAssay-method | Add Subobjects |
| sub-subset-Seurat-NULL | Remove Subobjects and Cell-Level Meta Data |
| sub-sub-.Seurat | Subobjects and Cell-Level Meta Data |
| sub-sub-.StdAssay | Feature-Level Meta Data |
| Theta | Get the offset angle |
| Tool | Get and Set Additional Tool Data |
| UpdateSeuratObject | Update old Seurat object to accommodate new features |
| UpdateSlots | Update slots in an object |
| v5-assay-summaries | V5 Assay Summaries |
| Version | Get Version Information |
| WhichCells | Identify cells matching certain criteria |
