Package: SeuratObject 4.1.4
Paul Hoffman
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> for more details.
Authors:
SeuratObject_4.1.4.tar.gz
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SeuratObject_4.1.4.tgz(r-4.4-arm64)SeuratObject_4.1.4.tgz(r-4.4-x86_64)SeuratObject_4.1.4.tgz(r-4.3-arm64)SeuratObject_4.1.4.tgz(r-4.3-x86_64)
SeuratObject_4.1.4.tar.gz(r-4.5-noble)SeuratObject_4.1.4.tar.gz(r-4.4-noble)
SeuratObject_4.1.4.tgz(r-4.4-emscripten)SeuratObject_4.1.4.tgz(r-4.3-emscripten)
SeuratObject.pdf |SeuratObject.html✨
SeuratObject/json (API)
NEWS
| # Install 'SeuratObject' in R: |
| install.packages('SeuratObject', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mojaveazure/seurat-object/issues
- pbmc_small - A small example version of the PBMC dataset
Last updated 10 months agofrom:9788970c57 (on v4.1.4)
Exports:.Contains.DefaultFOV%!na%%!NA%%||%%iff%%na%%NA%AddMetaDataas.Centroidsas.Graphas.Neighboras.Segmentationas.Seuratas.sparseAssaysAttachDepsBoundariesCellsCellsByIdentitiesCheckDotsCheckGCCheckMatrixcolMeanscolSumsCommandCreateAssayObjectCreateCentroidsCreateDimReducObjectCreateFOVCreateMoleculesCreateSegmentationCreateSeuratObjectCropDefaultAssayDefaultAssay<-DefaultBoundaryDefaultBoundary<-DefaultDimReducDefaultFOVDefaultFOV<-DegreesDistancesEmbeddingsEmptyDFFeaturesFetchDataFilterObjectsGetAssayDataGetImageGetTissueCoordinatesGraphshandlersHVFInfoIdentsIdents<-ImagesIndexIndex<-IndicesIsGlobalIsMatrixEmptyIsNamedListIsS4ListJSJS<-KeyKey<-KeysListToS4LoadingsLoadings<-LogMapLogSeuratCommandMatchCellsMiscMisc<-MoleculesNeighborsOverlayPackageCheckplanPolyVtxProjectProject<-RadiansRadiusRandomNameReductionsRenameAssaysRenameCellsRenameIdentsReorderIdentrowMeansRowMergeSparseMatricesrowSumsS4ToListSetAssayDataSetIdentshowSimplifySpatiallyVariableFeaturesStashIdentStdevSVFInfoThetaToolTool<-UpdateSeuratObjectUpdateSlotsVariableFeaturesVariableFeatures<-VersionWhichCellswith_progress
Dependencies:codetoolsdigestfuturefuture.applyglobalslatticelistenvMatrixparallellyprogressrRcppRcppEigenrlangsp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SeuratObject: Data Structures for Single Cell Data | SeuratObject-package SeuratObject |
| Add in metadata associated with either cells or features. | AddMetaData AddMetaData.Assay AddMetaData.Seurat SeuratAccess |
| Aggregate Molecules into an Expression Matrix | aggregate aggregate.FOV aggregate.Molecules |
| 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 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 |
| 'Assay' Methods | Assay-methods colMeans,Assay-method colSums,Assay-method dim.Assay dimnames.Assay head.Assay merge.Assay rowMeans,Assay-method rowSums,Assay-method show,Assay-method subset.Assay tail.Assay [.Assay [[.Assay [[<-,Assay,ANY,ANY,ANY-method |
| Get and Set Assay Data | AssayData GetAssayData GetAssayData.Assay GetAssayData.Seurat SetAssayData SetAssayData.Assay SetAssayData.Seurat |
| Query Specific Object Types | Assays 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 |
| Cell and Feature Names | Cells Cells.default Cells.DimReduc Cells.Neighbor Features |
| 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 |
| Get SeuratCommands | Command Command.Seurat |
| 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.default |
| Crop Coordinates | Crop Crop.FOV |
| Default Assay | DefaultAssay DefaultAssay.Assay DefaultAssay.DimReduc DefaultAssay.Graph DefaultAssay.Seurat DefaultAssay.SeuratCommand DefaultAssay<- DefaultAssay<-.Assay DefaultAssay<-.DimReduc DefaultAssay<-.Graph DefaultAssay<-.Seurat |
| Find the default 'DimReduc' | DefaultDimReduc |
| Get and Set the Default FOV | DefaultFOV DefaultFOV.Seurat DefaultFOV<- DefaultFOV<-.Seurat |
| The Dimensional Reduction Class | DimReduc DimReduc-class |
| 'DimReduc' Methods | dim.DimReduc dimnames.DimReduc DimReduc-methods length.DimReduc merge.DimReduc names.DimReduc print print.DimReduc show,DimReduc-method subset.DimReduc [.DimReduc [[.DimReduc |
| Get the Neighbor nearest neighbors distance matrix | Distances Distances.Neighbor |
| Get Cell Embeddings | Embeddings Embeddings.DimReduc Embeddings.Seurat |
| 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 |
| 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.Seurat SpatiallyVariableFeatures SpatiallyVariableFeatures.Assay SpatiallyVariableFeatures.Seurat SVFInfo SVFInfo.Assay SVFInfo.Seurat VariableFeatures VariableFeatures.Assay VariableFeatures.Seurat VariableFeatures<- VariableFeatures<-.Assay 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 |
| Is an object global/persistent? | IsGlobal IsGlobal.default IsGlobal.DimReduc |
| Check if a matrix is empty | IsMatrixEmpty |
| Check List Names | IsNamedList |
| The JackStrawData Class | JackStrawData JackStrawData-class |
| 'JackStrawData' Methods | $.JackStrawData .DollarNames.JackStrawData as.logical.JackStrawData JackStrawData-methods show,JackStrawData-method |
| Get and set JackStraw information | JS JS.DimReduc JS.JackStrawData JS<- JS<-.DimReduc JS<-.JackStrawData |
| Get and set object keys | Key Key.Assay Key.DimReduc Key.Seurat Key<- Key<-.Assay Key<-.DimReduc Keys Keys.Seurat |
| Get and set feature loadings | Loadings Loadings.DimReduc Loadings.Seurat Loadings<- Loadings<-.DimReduc |
| A Logical Map | LogMap LogMap-class show,LogMap-method [[,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 |
| Log a command | LogSeuratCommand |
| Match Cells | MatchCells MatchCells.character MatchCells.NULL MatchCells.numeric |
| Get and set miscellaneous data | Misc Misc.Assay Misc.DimReduc Misc.Seurat Misc<- Misc<-.Assay Misc<-.DimReduc Misc<-.Seurat |
| The Spatial Molecules Class | Molecules-class |
| 'Molecules' Methods | Features.Molecules GetTissueCoordinates.Molecules Molecules-methods show,Molecules-method subset.Molecules |
| 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 |
| 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.DimReduc RenameCells.Neighbor RenameCells.Seurat |
| Merge Sparse Matrices by Row | RowMergeSparseMatrices |
| S4/List Conversion | IsS4List ListToS4 s4list S4ToList S4ToList.default S4ToList.list |
| 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 'NA' | %!NA% %!na% %NA% %na% set-if-na |
| The Seurat Class | Seurat Seurat-class |
| Seurat Methods | $.Seurat $<-.Seurat .DollarNames.Seurat AddSamples colMeans,Seurat-method colSums,Seurat-method dim.Seurat dimnames.Seurat head.Seurat merge merge.Seurat MergeSeurat names.Seurat rowMeans,Seurat-method rowSums,Seurat-method Seurat-methods show,Seurat-method subset subset.Seurat tail.Seurat [.Seurat [[.Seurat [[<-,Seurat,ANY,ANY,ANY-method |
| The SeuratCommand Class | SeuratCommand SeuratCommand-class |
| 'SeuratCommand' Methods | $.SeuratCommand .DollarNames.SeuratCommand as.list.SeuratCommand SeuratCommand-methods show,SeuratCommand-method [.SeuratCommand |
| 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 |
| Get the standard deviations for an object | Stdev Stdev.DimReduc Stdev.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 |