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:Paul Hoffman [aut], Rahul Satija [aut, cre], David Collins [aut], Yuhan Hao [aut], Austin Hartman [aut], Gesmira Molla [aut], Andrew Butler [aut], Tim Stuart [aut], Madeline Kowalski [ctb], Saket Choudhary [ctb], Skylar Li [ctb], Longda Jiang [ctb], Jeff Farrell [ctb], Shiwei Zheng [ctb], Christoph Hafemeister [ctb], Patrick Roelli [ctb]

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NEWS

# Install 'SeuratObject' in R:
install.packages('SeuratObject', repos = c('https://mojaveazure.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

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

On CRAN:

11.86 score 24 stars 83 packages 1.0k scripts 43k downloads 2 mentions 158 exports 20 dependencies

Last updated 7 months agofrom:58bf437fe0 (on develop). Checks:OK: 1 ERROR: 5 NOTE: 3. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-win-x86_64ERRORNov 04 2024
R-4.5-linux-x86_64ERRORNov 04 2024
R-4.4-win-x86_64ERRORNov 04 2024
R-4.4-mac-x86_64ERRORNov 04 2024
R-4.4-mac-aarch64ERRORNov 04 2024
R-4.3-win-x86_64NOTENov 04 2024
R-4.3-mac-x86_64NOTENov 04 2024
R-4.3-mac-aarch64NOTENov 04 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 pageTopics
SeuratObject: Data Structures for Single Cell DataSeuratObject-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 Datahead.Assay tail.Assay [[.Assay [[<-,Assay,ANY,ANY,ANY-method [[<-,Assay,missing,missing,data.frame-method
Feature-Level Meta Datahead.Assay5 tail.Assay5 [[.Assay5 [[<-,Assay5,ANY,ANY,ANY-method
Get Cell Embeddings[[.DimReduc
Subobjects and Cell-Level Meta Datahead.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 Dataremove-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 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 a 'SeuratCommand' to a listas.list.SeuratCommand
Coerce Logical Maps to Matricesas.matrix.LogMap
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
V3 Assay ValidityAssay-validity
The v5 'Assay' ObjectAssay5 Assay5-class
V5 Assay ValidityAssay5-validity
Get and Set Assay DataAssayData GetAssayData GetAssayData.Assay GetAssayData.Seurat SetAssayData SetAssayData.Assay SetAssayData.Seurat
Query Specific Object TypesAssays Assays.Seurat Graphs Neighbors Reductions
Attach Required PackagesAttachDeps
Get, Set, and Query Segmentation BoundariesBoundaries Boundaries.FOV DefaultBoundary DefaultBoundary.FOV DefaultBoundary<- DefaultBoundary<-.FOV Molecules Molecules.FOV
Cast Assay LayersCastAssay CastAssay.Assay5
Cell and Feature NamesCells Cells.Assay5 Cells.default Cells.DimReduc Cells.Neighbor Features Features.Assay5
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
Check layers names for the input listCheckLayersName
Get SeuratCommandsCommand Command.Seurat
Create a v5 Assay objectCreateAssay5Object
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.Assay5 CreateSeuratObject.default
Crop CoordinatesCrop Crop.FOV
Default AssayDefaultAssay 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 FOVDefaultFOV DefaultFOV.Seurat DefaultFOV<- DefaultFOV<-.Seurat
Default LayerDefaultLayer DefaultLayer.Assay DefaultLayer.Assay5 DefaultLayer<- DefaultLayer<-.Assay5
Feature and Cell Numbersdim.Assay
Feature and Cell Numbersdim.Assay5
Dimensional Reduction Meta-Informationdim.DimReduc dimnames.DimReduc length.DimReduc names.DimReduc
Feature and Cell Numbersdim.Seurat
Assay-Level Feature and Cell Namesdimnames.Assay dimnames<-.Assay
Assay-Level Feature and Cell Namesdimnames.Assay5 dimnames<-.Assay5
Feature and Cell Namesdimnames.Seurat dimnames<-.Seurat
The Dimensional Reduction ClassDimReduc DimReduc-class
Dimensional Reduction ValidityDimReduc-validity
Get the Neighbor nearest neighbors distance matrixDistances Distances.Neighbor
Drop Unused Logical Map Valuesdroplevels.LogMap
Get Cell EmbeddingsEmbeddings Embeddings.DimReduc Embeddings.Seurat
Empty MatricesEmptyMatrix
Access cellular dataFetchData FetchData.DimReduc FetchData.Seurat
Find Sub-objects of a Certain ClassFilterObjects
The Field of View ObjectFOV FOV-class
'FOV' Methods$.FOV Cells.FOV Features.FOV FetchData.FOV FOV-methods GetTissueCoordinates.FOV Keys.FOV length.FOV names.FOV RenameCells.FOV show,FOV-method subset.FOV [.FOV [[.FOV [[<-,FOV,character,missing,Centroids-method [[<-,FOV,character,missing,Molecules-method [[<-,FOV,character,missing,NULL-method [[<-,FOV,character,missing,Segmentation-method
FOV ValidityFOV-validity
Get image dataGetImage GetImage.Seurat
Get tissue coordinatesGetTissueCoordinates GetTissueCoordinates.Seurat
The Graph ClassGraph Graph-class
Highly Variable FeaturesHVFInfo HVFInfo.Assay HVFInfo.Assay5 HVFInfo.Seurat SpatiallyVariableFeatures SpatiallyVariableFeatures.Assay SpatiallyVariableFeatures.Seurat SVFInfo SVFInfo.Assay SVFInfo.Seurat VariableFeatures VariableFeatures.Assay VariableFeatures.Assay5 VariableFeatures.Seurat VariableFeatures<- VariableFeatures<-.Assay VariableFeatures<-.Assay5 VariableFeatures<-.Seurat
Get, set, and manipulate an object's identity classesdroplevels.Seurat Idents Idents.Seurat Idents<- Idents<-.Seurat levels.Seurat levels<-.Seurat RenameIdent RenameIdents RenameIdents.Seurat ReorderIdent ReorderIdent.Seurat SetIdent SetIdent.Seurat StashIdent StashIdent.Seurat
Pull spatial image namesImages
Get Neighbor algorithm indexIndex Index.Neighbor Index<- Index<-.Neighbor
Get Neighbor nearest neighbor index matricesIndices Indices.Neighbor
Find Common Logical Map Valuesintersect.LogMap
Is an object global/persistent?IsGlobal IsGlobal.default IsGlobal.DimReduc
Check if a matrix is emptyIsMatrixEmpty IsMatrixEmpty.default
Check List NamesIsNamedList
The JackStrawData ClassJackStrawData JackStrawData-class
'JackStrawData' Methods$.JackStrawData .DollarNames.JackStrawData as.logical.JackStrawData JackStrawData-methods show,JackStrawData-method
Split and Join Layers TogetherJoinLayers JoinLayers.Assay5 JoinLayers.Seurat
Get and set JackStraw informationJS JS.DimReduc JS.JackStrawData JS<- JS<-.DimReduc JS<-.JackStrawData
Get and set object keysKey Key.Assay Key.Assay5 Key.DimReduc Key.Seurat Key<- Key<-.Assay Key<-.Assay5 Key<-.DimReduc Keys Keys.Seurat
Find Observations by Valuelabels.LogMap
Query and Manipulate Assay LayersLayerData LayerData.Assay LayerData.Assay5 LayerData.Seurat LayerData<- LayerData<-.Assay LayerData<-.Assay5 LayerData<-.Seurat Layers Layers.Assay Layers.Assay5 Layers.Seurat
Get and set feature loadingsLoadings Loadings.DimReduc Loadings.Seurat Loadings<- Loadings<-.DimReduc
A Logical MapLogMap 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 ValidityLogMap-validity
Log a commandLogSeuratCommand
Merge Assaysmerge.Assay
Merge Assaysmerge.Assay5
Merge Dimensional Reductionsmerge.DimReduc
Merge Seurat ObjectsAddSamples merge merge.Seurat MergeSeurat
Get and set miscellaneous dataMisc Misc.Assay Misc.Assay5 Misc.DimReduc Misc.Seurat Misc<- Misc<-.Assay Misc<-.Assay5 Misc<-.DimReduc Misc<-.Seurat
The Spatial Molecules ClassMolecules-class
'Molecules' MethodsFeatures.Molecules GetTissueCoordinates.Molecules Molecules-methods show,Molecules-method subset.Molecules
Subobject Namesnames.Seurat
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
Print Top Feature Loadingsprint print.DimReduc
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.Assay5 RenameCells.DimReduc RenameCells.Neighbor RenameCells.Seurat
Merge Sparse Matrices by RowRowMergeSparseMatrices
Save and Load 'Seurat' Objects from Rds filesLoadSeuratRds SaveSeuratRds
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 or If Not 'NULL'%iff% %||% set-if-null
The Seurat ClassSeurat Seurat-class
Seurat Object ValiditySeurat-validity
The 'SeuratCommand' ClassSeuratCommand SeuratCommand-class
'LogMap' Object Overviewshow,LogMap-method
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
Split an Assaysplit.Assay
Split an Assaysplit.Assay5
Get the standard deviations for an objectStdev Stdev.DimReduc Stdev.Seurat
Stitch Matrices TogetherStitchMatrix
Subset an Assaysubset.Assay
Subset an Assaysubset.Assay5
Subset a Dimensional Reductionsubset.DimReduc
Subset 'Seurat' Objectssubset subset.Seurat [.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