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:Rahul Satija [aut], Andrew Butler [aut], Paul Hoffman [aut, cre], Tim Stuart [aut], Jeff Farrell [ctb], Shiwei Zheng [ctb], Christoph Hafemeister [ctb], Patrick Roelli [ctb], Yuhan Hao [ctb]

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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'))

Peer review:

Bug tracker:https://github.com/mojaveazure/seurat-object/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • pbmc_small - A small example version of the PBMC dataset

On CRAN:

115 exports 20 stars 7.04 score 14 dependencies 115 dependents 63.5k downloads

Last updated 9 months agofrom:9788970c5789134cdf30d60b2a72d814f9304a84 (via 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 pageTopics
SeuratObject: Data Structures for Single Cell DataSeuratObject-package SeuratObject
Add in metadata associated with either cells or features.AddMetaData AddMetaData.Assay AddMetaData.Seurat SeuratAccess
Aggregate Molecules into an Expression Matrixaggregate aggregate.FOV aggregate.Molecules
Convert Segmentation Layersas.Centroids as.Centroids.Segmentation as.Segmentation as.Segmentation.Centroids
Coerce to a 'Graph' Objectas.Graph as.Graph.Matrix as.Graph.matrix as.Graph.Neighbor
Coerce to a 'Neighbor' Objectas.Neighbor as.Neighbor.Graph
Coerce to a 'Seurat' Objectas.Seurat
Cast to Sparseas.sparse as.sparse.data.frame as.sparse.Matrix as.sparse.matrix as.sparse.ngCMatrix
The Assay ClassAssay Assay-class
'Assay' MethodsAssay-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 DataAssayData GetAssayData GetAssayData.Assay GetAssayData.Seurat SetAssayData SetAssayData.Assay SetAssayData.Seurat
Query Specific Object TypesAssays Graphs Neighbors Reductions
Attach Required PackagesAttachDeps
Get, Set, and Query Segmentation BoundariesBoundaries Boundaries.FOV DefaultBoundary DefaultBoundary.FOV DefaultBoundary<- DefaultBoundary<-.FOV Molecules Molecules.FOV
Cell and Feature NamesCells Cells.default Cells.DimReduc Cells.Neighbor Features
Get cell names grouped by identity classCellsByIdentities
Get a vector of cell names associated with an image (or set of images)CellsByImage
The 'Centroids' ClassCentroids-class
'Centroids' MethodsCells.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 CollectionCheckGC
Get SeuratCommandsCommand Command.Seurat
Create an Assay objectCreateAssayObject
Create a 'Centroids' ObjectsCreateCentroids
Create a DimReduc objectCreateDimReducObject SetDimReduction
Create Spatial CoordinatesCreateFOV CreateFOV.Centroids CreateFOV.data.frame CreateFOV.list CreateFOV.Segmentation
Create a 'Molecules' ObjectCreateMolecules CreateMolecules.data.frame CreateMolecules.Molecules CreateMolecules.NULL
Create a 'Segmentation' ObjectsCreateSegmentation CreateSegmentation.data.frame CreateSegmentation.Segmentation
Create a 'Seurat' objectCreateSeuratObject CreateSeuratObject.Assay CreateSeuratObject.default
Crop CoordinatesCrop Crop.FOV
Default AssayDefaultAssay 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 FOVDefaultFOV DefaultFOV.Seurat DefaultFOV<- DefaultFOV<-.Seurat
The Dimensional Reduction ClassDimReduc DimReduc-class
'DimReduc' Methodsdim.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 matrixDistances Distances.Neighbor
Get Cell EmbeddingsEmbeddings Embeddings.DimReduc Embeddings.Seurat
Access cellular dataFetchData FetchData.DimReduc FetchData.Seurat
Find Sub-objects of a Certain ClassFilterObjects
The Field of View ObjectFOV FOV-class
'FOV' Methods$.FOV Cells.FOV Features.FOV FetchData.FOV FOV-methods GetTissueCoordinates.FOV Keys.FOV length.FOV names.FOV RenameCells.FOV show,FOV-method subset.FOV [.FOV [[.FOV [[<-,FOV,character,missing,Centroids-method [[<-,FOV,character,missing,Molecules-method [[<-,FOV,character,missing,NULL-method [[<-,FOV,character,missing,Segmentation-method
Get image dataGetImage GetImage.Seurat
Get tissue coordinatesGetTissueCoordinates GetTissueCoordinates.Seurat
The Graph ClassGraph Graph-class
Highly Variable FeaturesHVFInfo HVFInfo.Assay HVFInfo.Seurat SpatiallyVariableFeatures SpatiallyVariableFeatures.Assay SpatiallyVariableFeatures.Seurat SVFInfo SVFInfo.Assay SVFInfo.Seurat VariableFeatures VariableFeatures.Assay VariableFeatures.Seurat VariableFeatures<- VariableFeatures<-.Assay VariableFeatures<-.Seurat
Get, set, and manipulate an object's identity classesdroplevels.Seurat Idents Idents.Seurat Idents<- Idents<-.Seurat levels.Seurat levels<-.Seurat RenameIdent RenameIdents RenameIdents.Seurat ReorderIdent ReorderIdent.Seurat SetIdent SetIdent.Seurat StashIdent StashIdent.Seurat
Pull spatial image namesImages
Get Neighbor algorithm indexIndex Index.Neighbor Index<- Index<-.Neighbor
Get Neighbor nearest neighbor index matricesIndices Indices.Neighbor
Is an object global/persistent?IsGlobal IsGlobal.default IsGlobal.DimReduc
Check if a matrix is emptyIsMatrixEmpty
Check List NamesIsNamedList
The JackStrawData ClassJackStrawData JackStrawData-class
'JackStrawData' Methods$.JackStrawData .DollarNames.JackStrawData as.logical.JackStrawData JackStrawData-methods show,JackStrawData-method
Get and set JackStraw informationJS JS.DimReduc JS.JackStrawData JS<- JS<-.DimReduc JS<-.JackStrawData
Get and set object keysKey Key.Assay Key.DimReduc Key.Seurat Key<- Key<-.Assay Key<-.DimReduc Keys Keys.Seurat
Get and set feature loadingsLoadings Loadings.DimReduc Loadings.Seurat Loadings<- Loadings<-.DimReduc
A Logical MapLogMap 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 commandLogSeuratCommand
Match CellsMatchCells MatchCells.character MatchCells.NULL MatchCells.numeric
Get and set miscellaneous dataMisc Misc.Assay Misc.DimReduc Misc.Seurat Misc<- Misc<-.Assay Misc<-.DimReduc Misc<-.Seurat
The Spatial Molecules ClassMolecules-class
'Molecules' MethodsFeatures.Molecules GetTissueCoordinates.Molecules Molecules-methods show,Molecules-method subset.Molecules
The Neighbor classNeighbor Neighbor-class
'Neighbor' Methodsdim.Neighbor Neighbor-methods show,Neighbor-method
Overlay 'Spatial' Objects Over One AnotherOverlay 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 packagePackageCheck
A small example version of the PBMC datasetpbmc_small
Get and set project informationProject Project.Seurat Project<- Project<-.Seurat
Get the spot radius from an imageRadius
Generate a random nameRandomName
Rename assays in a 'Seurat' objectRenameAssays
Rename cellsRenameCells RenameCells.Assay RenameCells.DimReduc RenameCells.Neighbor RenameCells.Seurat
Merge Sparse Matrices by RowRowMergeSparseMatrices
S4/List ConversionIsS4List ListToS4 s4list S4ToList S4ToList.default S4ToList.list
The 'Segmentation' ClassSegmentation-class
'Segmentation' MethodsCells.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 ClassSeurat Seurat-class
Seurat Methods$.Seurat $<-.Seurat .DollarNames.Seurat AddSamples colMeans,Seurat-method colSums,Seurat-method dim.Seurat dimnames.Seurat head.Seurat merge merge.Seurat MergeSeurat names.Seurat rowMeans,Seurat-method rowSums,Seurat-method Seurat-methods show,Seurat-method subset subset.Seurat tail.Seurat [.Seurat [[.Seurat [[<-,Seurat,ANY,ANY,ANY-method
The SeuratCommand ClassSeuratCommand SeuratCommand-class
'SeuratCommand' Methods$.SeuratCommand .DollarNames.SeuratCommand as.list.SeuratCommand SeuratCommand-methods show,SeuratCommand-method [.SeuratCommand
Simplify GeometrySimplify Simplify.Spatial
The SpatialImage classSpatialImage SpatialImage-class
'SpatialImage' methodsCells.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 objectStdev Stdev.DimReduc Stdev.Seurat
Get the offset angleTheta
Get and set additional tool dataTool Tool.Seurat Tool<- Tool<-.Seurat Tools
Update old Seurat object to accommodate new featuresUpdateSeuratObject
Update slots in an objectUpdateSlots
Get Version InformationVersion Version.Seurat
Identify cells matching certain criteriaWhichCells WhichCells.Assay WhichCells.Seurat