Package: SeuratObject 5.0.2
Rahul Satija
SeuratObject: Data Structures for Single Cell Data
Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.
Authors:
SeuratObject_5.0.2.tar.gz
SeuratObject_5.0.2.zip(r-4.5)SeuratObject_5.0.2.zip(r-4.4)SeuratObject_5.0.2.zip(r-4.3)
SeuratObject_5.0.2.tgz(r-4.4-x86_64)SeuratObject_5.0.2.tgz(r-4.4-arm64)SeuratObject_5.0.2.tgz(r-4.3-x86_64)SeuratObject_5.0.2.tgz(r-4.3-arm64)
SeuratObject_5.0.2.tar.gz(r-4.5-noble)SeuratObject_5.0.2.tar.gz(r-4.4-noble)
SeuratObject_5.0.2.tgz(r-4.4-emscripten)
SeuratObject.pdf |SeuratObject.html✨
SeuratObject/json (API)
NEWS
| # Install 'SeuratObject' in R: |
| install.packages('SeuratObject', repos = c('https://mojaveazure.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/satijalab/seurat-object/issues
Datasets:
- pbmc_small - A small example version of the PBMC dataset
Last updated 4 months agofrom:58bf437fe0 (on develop). Checks:OK: 9. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 05 2024 |
| R-4.5-win-x86_64 | OK | Sep 05 2024 |
| R-4.5-linux-x86_64 | OK | Sep 05 2024 |
| R-4.4-win-x86_64 | OK | Sep 05 2024 |
| R-4.4-mac-x86_64 | OK | Sep 05 2024 |
| R-4.4-mac-aarch64 | OK | Sep 05 2024 |
| R-4.3-win-x86_64 | OK | Sep 05 2024 |
| R-4.3-mac-x86_64 | OK | Sep 05 2024 |
| R-4.3-mac-aarch64 | OK | Sep 05 2024 |
Exports:.AssayClass.BPMatrixMode.CalcN.CheckFmargin.ClassPkg.Collections.Contains.CreateStdAssay.DefaultFOV.Deprecate.DiskLoad.FileMove.FilePath.FilterObjects.FindObject.GetMethod.IsFutureSeurat.KeyPattern.MARGIN.PropagateList.RandomKey.SelectFeatures.SparseSlots.Subobjects%!na%%!NA%%||%%iff%%na%%NA%AddMetaDataas.Centroidsas.Graphas.Neighboras.Segmentationas.Seuratas.sparseAssaysAttachDepsBoundariesCastAssayCellsCellsByIdentitiesCheckDotsCheckFeaturesNamesCheckGCCheckLayersNameCheckMatrixClassKeycolMeanscolSumsCommandCreateAssay5ObjectCreateAssayObjectCreateCentroidsCreateDimReducObjectCreateFOVCreateMoleculesCreateSegmentationCreateSeuratObjectCropDefaultAssayDefaultAssay<-DefaultBoundaryDefaultBoundary<-DefaultDimReducDefaultFOVDefaultFOV<-DefaultLayerDefaultLayer<-DegreesDistancesEmbeddingsEmptyDFEmptyMatrixExtractFieldFeaturesFetchDataFilterObjectsGetAssayDataGetImageGetTissueCoordinatesGraphshandlersHVFInfoIdentsIdents<-ImagesIndexIndex<-IndicesintersectIsGlobalIsMatrixEmptyIsNamedListIsS4ListIsSparseJoinLayersJSJS<-KeyKey<-KeysLayerDataLayerData<-LayersListToS4LoadingsLoadings<-LoadSeuratRdsLogMapLogSeuratCommandMatchCellsMiscMisc<-MoleculesNeighborsOverlayPackageCheckplanPolyVtxProjectProject<-RadiansRadiusRandomNameReductionsRegisterSparseMatrixRenameAssaysRenameCellsRenameIdentsReorderIdentrowMeansRowMergeSparseMatricesrowSumsS4ToListSaveSeuratRdsSetAssayDataSetIdentshowSimplifySparseEmptyMatrixSpatiallyVariableFeaturesStashIdentStdevStitchMatrixSVFInfotThetaToolTool<-UpdateSeuratObjectUpdateSlotsVariableFeaturesVariableFeatures<-VersionWhichCellswith_progress
Dependencies:clicodetoolsdigestdotCall64futurefuture.applygenericsglobalsgluelatticelifecyclelistenvMatrixparallellyprogressrRcppRcppEigenrlangspspam
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SeuratObject: Data Structures for Single Cell Data | SeuratObject-package SeuratObject |
| Dollar-sign Autocompletion | .DollarNames.SeuratCommand |
| Layer Data | [.Assay [<-,Assay,character,ANY,ANY-method |
| Layer Data | [.Assay5 [<-,Assay5,character,ANY,ANY-method |
| Get Feature Loadings | [.DimReduc |
| Command Log Data Access | [.SeuratCommand |
| Feature-Level Meta Data | head.Assay tail.Assay [[.Assay [[<-,Assay,ANY,ANY,ANY-method [[<-,Assay,missing,missing,data.frame-method |
| Feature-Level Meta Data | head.Assay5 tail.Assay5 [[.Assay5 [[<-,Assay5,ANY,ANY,ANY-method |
| Get Cell Embeddings | [[.DimReduc |
| Subobjects and Cell-Level Meta Data | head.Seurat tail.Seurat [[.Seurat |
| Add Subobjects | [[<-,Seurat [[<-,Seurat,character,missing,Assay-method [[<-,Seurat,character,missing,Assay5-method [[<-,Seurat,character,missing,DimReduc-method [[<-,Seurat,character,missing,Graph-method [[<-,Seurat,character,missing,Neighbor-method [[<-,Seurat,character,missing,SeuratCommand-method [[<-,Seurat,character,missing,SpatialImage-method [[<-.Seurat \S4method{[[<-}{Seurat,character,missing,Assay} |
| Remove Subobjects and Cell-Level Meta Data | remove-object remove-objects [[<-,Seurat,character,missing,NULL-method [[<-,Seurat,NULL \S4method{[[<-}{Seurat,character,missing,NULL} |
| Layer Data | $.Assay $<-.Assay |
| Layer Data | $.Assay5 $<-.Assay5 |
| Cell-Level Meta Data | $.Seurat $<-.Seurat [[<-,Seurat,character,missing,data.frame-method [[<-,Seurat,character,missing,factor-method [[<-,Seurat,character,missing,list-method [[<-,Seurat,character,missing,vector-method [[<-,Seurat,missing,missing,data.frame-method [[<-,Seurat,missing,missing,list-method |
| Command Log Parameter Access | $.SeuratCommand |
| Add in metadata associated with either cells or features. | AddMetaData AddMetaData.Assay AddMetaData.Assay5 AddMetaData.Seurat SeuratAccess |
| Convert Segmentation Layers | as.Centroids as.Centroids.Segmentation as.Segmentation as.Segmentation.Centroids |
| Coerce to a 'Graph' Object | as.Graph as.Graph.Matrix as.Graph.matrix as.Graph.Neighbor |
| Coerce a 'SeuratCommand' to a list | as.list.SeuratCommand |
| Coerce Logical Maps to Matrices | as.matrix.LogMap |
| Coerce to a 'Neighbor' Object | as.Neighbor as.Neighbor.Graph |
| Coerce to a 'Seurat' Object | as.Seurat |
| Cast to Sparse | as.sparse as.sparse.data.frame as.sparse.Matrix as.sparse.matrix as.sparse.ngCMatrix |
| The Assay Class | Assay Assay-class |
| V3 Assay Validity | Assay-validity |
| The v5 'Assay' Object | Assay5 Assay5-class |
| V5 Assay Validity | Assay5-validity |
| Get and Set Assay Data | AssayData GetAssayData GetAssayData.Assay GetAssayData.Seurat SetAssayData SetAssayData.Assay SetAssayData.Seurat |
| Query Specific Object Types | Assays Assays.Seurat Graphs Neighbors Reductions |
| Attach Required Packages | AttachDeps |
| Get, Set, and Query Segmentation Boundaries | Boundaries Boundaries.FOV DefaultBoundary DefaultBoundary.FOV DefaultBoundary<- DefaultBoundary<-.FOV Molecules Molecules.FOV |
| Cast Assay Layers | CastAssay CastAssay.Assay5 |
| Cell and Feature Names | Cells Cells.Assay5 Cells.default Cells.DimReduc Cells.Neighbor Features Features.Assay5 |
| Get cell names grouped by identity class | CellsByIdentities |
| Get a vector of cell names associated with an image (or set of images) | CellsByImage |
| The 'Centroids' Class | Centroids-class |
| 'Centroids' Methods | Cells.Centroids Centroids-methods GetTissueCoordinates.Centroids is.finite.Centroids is.infinite.Centroids length.Centroids lengths.Centroids Radius.Centroids RenameCells.Centroids show,Centroids-method subset.Centroids Theta.Centroids [,Centroids,character,ANY,ANY-method [,Centroids,numeric,ANY,ANY-method |
| Conditional Garbage Collection | CheckGC |
| Check layers names for the input list | CheckLayersName |
| Get SeuratCommands | Command Command.Seurat |
| Create a v5 Assay object | CreateAssay5Object |
| Create an Assay object | CreateAssayObject |
| Create a 'Centroids' Objects | CreateCentroids |
| Create a DimReduc object | CreateDimReducObject SetDimReduction |
| Create Spatial Coordinates | CreateFOV CreateFOV.Centroids CreateFOV.data.frame CreateFOV.list CreateFOV.Segmentation |
| Create a 'Molecules' Object | CreateMolecules CreateMolecules.data.frame CreateMolecules.Molecules CreateMolecules.NULL |
| Create a 'Segmentation' Objects | CreateSegmentation CreateSegmentation.data.frame CreateSegmentation.Segmentation |
| Create a 'Seurat' object | CreateSeuratObject CreateSeuratObject.Assay CreateSeuratObject.Assay5 CreateSeuratObject.default |
| Crop Coordinates | Crop Crop.FOV |
| Default Assay | DefaultAssay DefaultAssay.Assay DefaultAssay.Assay5 DefaultAssay.DimReduc DefaultAssay.Graph DefaultAssay.Seurat DefaultAssay.SeuratCommand DefaultAssay<- DefaultAssay<-.Assay DefaultAssay<-.Assay5 DefaultAssay<-.DimReduc DefaultAssay<-.Graph DefaultAssay<-.Seurat |
| Find the default 'DimReduc' | DefaultDimReduc |
| Get and Set the Default FOV | DefaultFOV DefaultFOV.Seurat DefaultFOV<- DefaultFOV<-.Seurat |
| Default Layer | DefaultLayer DefaultLayer.Assay DefaultLayer.Assay5 DefaultLayer<- DefaultLayer<-.Assay5 |
| Feature and Cell Numbers | dim.Assay |
| Feature and Cell Numbers | dim.Assay5 |
| Dimensional Reduction Meta-Information | dim.DimReduc dimnames.DimReduc length.DimReduc names.DimReduc |
| Feature and Cell Numbers | dim.Seurat |
| Assay-Level Feature and Cell Names | dimnames.Assay dimnames<-.Assay |
| Assay-Level Feature and Cell Names | dimnames.Assay5 dimnames<-.Assay5 |
| Feature and Cell Names | dimnames.Seurat dimnames<-.Seurat |
| The Dimensional Reduction Class | DimReduc DimReduc-class |
| Dimensional Reduction Validity | DimReduc-validity |
| Get the Neighbor nearest neighbors distance matrix | Distances Distances.Neighbor |
| Drop Unused Logical Map Values | droplevels.LogMap |
| Get Cell Embeddings | Embeddings Embeddings.DimReduc Embeddings.Seurat |
| Empty Matrices | EmptyMatrix |
| Access cellular data | FetchData FetchData.DimReduc FetchData.Seurat |
| Find Sub-objects of a Certain Class | FilterObjects |
| The Field of View Object | FOV FOV-class |
| 'FOV' Methods | $.FOV Cells.FOV Features.FOV FetchData.FOV FOV-methods GetTissueCoordinates.FOV Keys.FOV length.FOV names.FOV RenameCells.FOV show,FOV-method subset.FOV [.FOV [[.FOV [[<-,FOV,character,missing,Centroids-method [[<-,FOV,character,missing,Molecules-method [[<-,FOV,character,missing,NULL-method [[<-,FOV,character,missing,Segmentation-method |
| FOV Validity | FOV-validity |
| Get image data | GetImage GetImage.Seurat |
| Get tissue coordinates | GetTissueCoordinates GetTissueCoordinates.Seurat |
| The Graph Class | Graph Graph-class |
| Highly Variable Features | HVFInfo HVFInfo.Assay HVFInfo.Assay5 HVFInfo.Seurat SpatiallyVariableFeatures SpatiallyVariableFeatures.Assay SpatiallyVariableFeatures.Seurat SVFInfo SVFInfo.Assay SVFInfo.Seurat VariableFeatures VariableFeatures.Assay VariableFeatures.Assay5 VariableFeatures.Seurat VariableFeatures<- VariableFeatures<-.Assay VariableFeatures<-.Assay5 VariableFeatures<-.Seurat |
| Get, set, and manipulate an object's identity classes | droplevels.Seurat Idents Idents.Seurat Idents<- Idents<-.Seurat levels.Seurat levels<-.Seurat RenameIdent RenameIdents RenameIdents.Seurat ReorderIdent ReorderIdent.Seurat SetIdent SetIdent.Seurat StashIdent StashIdent.Seurat |
| Pull spatial image names | Images |
| Get Neighbor algorithm index | Index Index.Neighbor Index<- Index<-.Neighbor |
| Get Neighbor nearest neighbor index matrices | Indices Indices.Neighbor |
| Find Common Logical Map Values | intersect.LogMap |
| Is an object global/persistent? | IsGlobal IsGlobal.default IsGlobal.DimReduc |
| Check if a matrix is empty | IsMatrixEmpty IsMatrixEmpty.default |
| Check List Names | IsNamedList |
| The JackStrawData Class | JackStrawData JackStrawData-class |
| 'JackStrawData' Methods | $.JackStrawData .DollarNames.JackStrawData as.logical.JackStrawData JackStrawData-methods show,JackStrawData-method |
| Split and Join Layers Together | JoinLayers JoinLayers.Assay5 JoinLayers.Seurat |
| Get and set JackStraw information | JS JS.DimReduc JS.JackStrawData JS<- JS<-.DimReduc JS<-.JackStrawData |
| Get and set object keys | Key Key.Assay Key.Assay5 Key.DimReduc Key.Seurat Key<- Key<-.Assay Key<-.Assay5 Key<-.DimReduc Keys Keys.Seurat |
| Find Observations by Value | labels.LogMap |
| Query and Manipulate Assay Layers | LayerData LayerData.Assay LayerData.Assay5 LayerData.Seurat LayerData<- LayerData<-.Assay LayerData<-.Assay5 LayerData<-.Seurat Layers Layers.Assay Layers.Assay5 Layers.Seurat |
| Get and set feature loadings | Loadings Loadings.DimReduc Loadings.Seurat Loadings<- Loadings<-.DimReduc |
| A Logical Map | LogMap LogMap-class [[,LogMap,character,missing-method [[,LogMap,missing,missing-method [[,LogMap,NULL,missing-method [[<-,LogMap,character,missing,character-method [[<-,LogMap,character,missing,integer-method [[<-,LogMap,character,missing,NULL-method [[<-,LogMap,character,missing,numeric-method |
| Logical Map Validity | LogMap-validity |
| Log a command | LogSeuratCommand |
| Merge Assays | merge.Assay |
| Merge Assays | merge.Assay5 |
| Merge Dimensional Reductions | merge.DimReduc |
| Merge Seurat Objects | AddSamples merge merge.Seurat MergeSeurat |
| Get and set miscellaneous data | Misc Misc.Assay Misc.Assay5 Misc.DimReduc Misc.Seurat Misc<- Misc<-.Assay Misc<-.Assay5 Misc<-.DimReduc Misc<-.Seurat |
| The Spatial Molecules Class | Molecules-class |
| 'Molecules' Methods | Features.Molecules GetTissueCoordinates.Molecules Molecules-methods show,Molecules-method subset.Molecules |
| Subobject Names | names.Seurat |
| The Neighbor class | Neighbor Neighbor-class |
| 'Neighbor' Methods | dim.Neighbor Neighbor-methods show,Neighbor-method |
| Overlay 'Spatial' Objects Over One Another | Overlay Overlay,Centroids,SpatialPolygons-method Overlay,FOV,FOV-method Overlay,FOV,Spatial-method Overlay,FOV,SpatialPolygons-method Overlay,Molecules,SpatialPolygons-method Overlay,Segmentation,SpatialPolygons-method |
| Check the existence of a package | PackageCheck |
| A small example version of the PBMC dataset | pbmc_small |
| Print Top Feature Loadings | print print.DimReduc |
| Get and set project information | Project Project.Seurat Project<- Project<-.Seurat |
| Get the spot radius from an image | Radius |
| Generate a random name | RandomName |
| Rename assays in a 'Seurat' object | RenameAssays |
| Rename cells | RenameCells RenameCells.Assay RenameCells.Assay5 RenameCells.DimReduc RenameCells.Neighbor RenameCells.Seurat |
| Merge Sparse Matrices by Row | RowMergeSparseMatrices |
| Save and Load 'Seurat' Objects from Rds files | LoadSeuratRds SaveSeuratRds |
| The 'Segmentation' Class | Segmentation-class |
| 'Segmentation' Methods | Cells.Segmentation coordinates,Segmentation-method GetTissueCoordinates.Segmentation lengths.Segmentation RenameCells.Segmentation Segmentation-methods show,Segmentation-method subset.Segmentation [,Segmentation,ANY,ANY,ANY-method |
| Set If or If Not 'NULL' | %iff% %||% set-if-null |
| The Seurat Class | Seurat Seurat-class |
| Seurat Object Validity | Seurat-validity |
| The 'SeuratCommand' Class | SeuratCommand SeuratCommand-class |
| 'LogMap' Object Overview | show,LogMap-method |
| Simplify Geometry | Simplify Simplify.Spatial |
| The SpatialImage class | SpatialImage SpatialImage-class |
| 'SpatialImage' methods | Cells.SpatialImage DefaultAssay.SpatialImage DefaultAssay<-.SpatialImage dim.SpatialImage GetImage.SpatialImage GetTissueCoordinates.SpatialImage IsGlobal.SpatialImage Key.SpatialImage Key<-.SpatialImage Radius.SpatialImage RenameCells.SpatialImage show,SpatialImage-method SpatialImage-methods subset.SpatialImage [.SpatialImage |
| Split an Assay | split.Assay |
| Split an Assay | split.Assay5 |
| Get the standard deviations for an object | Stdev Stdev.DimReduc Stdev.Seurat |
| Stitch Matrices Together | StitchMatrix |
| Subset an Assay | subset.Assay |
| Subset an Assay | subset.Assay5 |
| Subset a Dimensional Reduction | subset.DimReduc |
| Subset 'Seurat' Objects | subset subset.Seurat [.Seurat |
| Get the offset angle | Theta |
| Get and Set Additional Tool Data | Tool Tool.Seurat Tool<- Tool<-.Seurat Tools |
| Update old Seurat object to accommodate new features | UpdateSeuratObject |
| Update slots in an object | UpdateSlots |
| Get Version Information | Version Version.Seurat |
| Identify cells matching certain criteria | WhichCells WhichCells.Assay WhichCells.Seurat |