{ "_id": "6a2746e324555f66ed52fc12", "Package": "SeuratObject", "Title": "Data Structures for Single Cell Data", "Version": "5.4.0.9001", "Authors@R": "c(\nperson(given = 'Paul', family = 'Hoffman', email = 'hoff0792@alumni.umn.edu', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),\nperson(given = 'Rahul', family = 'Satija', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),\nperson(given = 'David', family = 'Collins', email = 'dcollins@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9243-7821')),\nperson(given = \"Yuhan\", family = \"Hao\", email = 'yhao@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0002-1810-0822')),\nperson(given = \"Austin\", family = \"Hartman\", email = 'ahartman@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-7278-1852')),\nperson(given = \"Gesmira\", family = \"Molla\", email = 'gmolla@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0002-8628-5056')),\nperson(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),\nperson(given = 'Tim', family = 'Stuart', email = 'tstuart@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),\nperson(given = \"Madeline\", family = \"Kowalski\", email = \"mkowalski@nygenome.org\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5655-7620\")),\nperson(given = \"Saket\", family = \"Choudhary\", email = \"schoudhary@nygenome.org\", role = \"ctb\", comment = c(ORCID = \"0000-0001-5202-7633\")),\nperson(given = \"Skylar\", family = \"Li\", email = \"sli@nygenome.org\", role = \"ctb\"),\nperson(given = \"Longda\", family = \"Jiang\", email = \"ljiang@nygenome.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4964-6497\")),\nperson(given = \"Anagha\", family = \"Shenoy\", email = \"ashenoy@nygenome.org\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0537-6862\")),\nperson(given = 'Jeff', family = 'Farrell', email = 'jfarrell@g.harvard.edu', role = 'ctb'),\nperson(given = 'Shiwei', family = 'Zheng', email = 'szheng@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),\nperson(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),\nperson(given = 'Patrick', family = 'Roelli', email = 'proelli@nygenome.org', role = 'ctb')\n)", "Description": "Defines S4 classes for single-cell genomic data and\nassociated information, such as dimensionality reduction\nembeddings, nearest-neighbor graphs, and spatially-resolved\ncoordinates. Provides data access methods and R-native hooks to\nensure the Seurat object is familiar to other R users. See\nSatija R, Farrell J, Gennert D, et al (2015)\n, Macosko E, Basu A, Satija R, et al\n(2015) , and Stuart T, Butler\nA, et al (2019) , Hao Y, Hao S,\net al (2021) and Hao Y, et al\n(2023) for more details.", "License": "MIT + file LICENSE", "URL": "https://satijalab.github.io/seurat-object/,\nhttps://github.com/satijalab/seurat-object", "BugReports": "https://github.com/satijalab/seurat-object/issues", "Additional_repositories": "https://bnprks.r-universe.dev", "Config/Needs/website": "pkgdown", "BuildManual": "true", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Collate": "'RcppExports.R' 'zzz.R' 'generics.R' 'keymixin.R' 'graph.R'\n'default.R' 'assay.R' 'logmap.R' 'layers.R' 'assay5.R'\n'centroids.R' 'command.R' 'compliance.R' 'data.R' 'jackstraw.R'\n'dimreduc.R' 'segmentation.R' 'molecules.R' 'spatial.R' 'fov.R'\n'neighbor.R' 'seurat.R' 'sparse.R' 'utils.R'", "Repository": "https://mojaveazure.r-universe.dev", "Date/Publication": "2026-06-08 21:03:13 UTC", 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"neighbor" ], "topics": [ "as.Neighbor", "as.Neighbor.Graph" ] }, { "page": "as.Seurat", "title": "Coerce to a 'Seurat' Object", "concept": [ "seurat" ], "topics": [ "as.Seurat" ] }, { "page": "as.sparse", "title": "Cast to Sparse", "concept": [ "utils" ], "topics": [ "as.sparse", "as.sparse.data.frame", "as.sparse.Matrix", "as.sparse.matrix", "as.sparse.ngCMatrix" ] }, { "page": "Assay-class", "title": "The Assay Class", "concept": [ "assay" ], "topics": [ "Assay", "Assay-class" ] }, { "page": "Assay-validity", "title": "V3 Assay Validity", "concept": [ "assay" ], "topics": [ "Assay-validity" ] }, { "page": "Assay5-class", "title": "The v5 'Assay' Object", "concept": [ "assay5" ], "topics": [ "Assay5", "Assay5-class" ] }, { "page": "Assay5-validity", "title": "V5 Assay Validity", "concept": [ "assay5" ], "topics": [ "Assay5-validity" ] }, { "page": "AssayData", "title": "Get and Set Assay Data", "concept": [ "data-access" ], "topics": [ "AssayData", "GetAssayData", "GetAssayData.Assay", "GetAssayData.Seurat", "SetAssayData", "SetAssayData.Assay", "SetAssayData.Seurat" ] }, { "page": "ObjectAccess", "title": "Query Specific Object Types", "concept": [ "data-access" ], "topics": [ "Assays", "Assays.Seurat", "Graphs", "Neighbors", "Reductions" ] }, { "page": "AttachDeps", "title": "Attach Required Packages", "concept": [ "utils" ], "topics": [ "AttachDeps" ] }, { "page": "Boundaries", "title": "Get, Set, and Query Segmentation Boundaries", "concept": [ "spatial" ], "topics": [ "Boundaries", "Boundaries.FOV", "DefaultBoundary", "DefaultBoundary.FOV", "DefaultBoundary<-", "DefaultBoundary<-.FOV", "Molecules", "Molecules.FOV" ] }, { "page": "CastAssay", "title": "Cast Assay Layers", "concept": [ "assay5" ], "topics": [ "CastAssay", "CastAssay.Assay5" ] }, { "page": "Cells", "title": "Cell and Feature Names", "concept": [ "data-access", "dimnames" ], "topics": [ "Cells", "Cells.Assay5", "Cells.default", "Cells.DimReduc", "Cells.Neighbor", "Features", "Features.Assay5" ] }, { "page": "CellsByIdentities", "title": "Get cell names grouped by identity class", "concept": [ "data-access" ], "topics": [ "CellsByIdentities" ] }, { "page": "CellsByImage", "title": "Get a vector of cell names associated with an image (or set of images)", "concept": [ "data-access" ], "topics": [ "CellsByImage" ] }, { "page": "Centroids-class", "title": "The 'Centroids' Class", "concept": [ "segmentation" ], "topics": [ "Centroids-class" ] }, { "page": "Centroids-methods", "title": "'Centroids' Methods", "concept": [ "segmentation" ], "topics": [ "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" ] }, { "page": "CheckGC", "title": "Conditional Garbage Collection", "concept": [ "utils" ], "topics": [ "CheckGC" ] }, { "page": "CheckLayersName", "title": "Check layers names for the input list", "concept": [ "utils" ], "topics": [ "CheckLayersName" ] }, { "page": "Command", "title": "Get SeuratCommands", "concept": [ "data-access" ], "topics": [ "Command", "Command.Seurat" ] }, { "page": "CreateAssay5Object", "title": "Create a v5 Assay object", "concept": [ "assay" ], "topics": [ "CreateAssay5Object" ] }, { "page": "CreateAssayObject", "title": "Create an Assay object", "concept": [ "assay" ], "topics": [ "CreateAssayObject" ] }, { "page": "CreateCentroids", "title": "Create a 'Centroids' Objects", "concept": [ "spatial" ], "topics": [ "CreateCentroids" ] }, { "page": "CreateDimReducObject", "title": "Create a DimReduc object", "concept": [ "dimreduc" ], "topics": [ "CreateDimReducObject", "SetDimReduction" ] }, { "page": "CreateFOV", "title": "Create Spatial Coordinates", "concept": [ "spatial" ], "topics": [ "CreateFOV", "CreateFOV.Centroids", "CreateFOV.data.frame", "CreateFOV.list", "CreateFOV.Segmentation" ] }, { "page": "CreateMolecules", "title": "Create a 'Molecules' Object", "concept": [ "spatial" ], "topics": [ "CreateMolecules", "CreateMolecules.data.frame", "CreateMolecules.Molecules", "CreateMolecules.NULL" ] }, { "page": "CreateSegmentation", "title": "Create a 'Segmentation' Objects", "concept": [ "spatial" ], "topics": [ "CreateSegmentation", "CreateSegmentation.data.frame", "CreateSegmentation.Segmentation", "CreateSegmentation.sf" ] }, { "page": "CreateSeuratObject", "title": "Create a 'Seurat' object", "concept": [ "seurat" ], "topics": [ "CreateSeuratObject", "CreateSeuratObject.Assay", "CreateSeuratObject.Assay5", "CreateSeuratObject.default" ] }, { "page": "Crop", "title": "Crop Coordinates", "concept": [ "spatial" ], "topics": [ "Crop", "Crop.FOV" ] }, { "page": "DefaultAssay", "title": "Default Assay", "concept": [ "data-access" ], "topics": [ "DefaultAssay", "DefaultAssay.Assay", "DefaultAssay.Assay5", "DefaultAssay.DimReduc", "DefaultAssay.Graph", "DefaultAssay.Seurat", "DefaultAssay.SeuratCommand", "DefaultAssay<-", "DefaultAssay<-.Assay", "DefaultAssay<-.Assay5", "DefaultAssay<-.DimReduc", "DefaultAssay<-.Graph", "DefaultAssay<-.Seurat" ] }, { "page": "DefaultDimReduc", "title": "Set Default Dimensionality Reduction Set the default dimensionality reduction for a specific assay in a Seurat object.", "concept": [ "utils" ], "topics": [ "DefaultDimReduc", "DefaultDimReduc<-", "DefaultDimReduc<-.Seurat" ] }, { "page": "DefaultFOV", "title": "Get and Set the Default FOV", "concept": [ "spatial" ], "topics": [ "DefaultFOV", "DefaultFOV.Seurat", "DefaultFOV<-", "DefaultFOV<-.Seurat" ] }, { "page": "DefaultLayer", "title": "Default Layer", "concept": [ "assay5" ], "topics": [ "DefaultLayer", "DefaultLayer.Assay", "DefaultLayer.Assay5", "DefaultLayer<-", "DefaultLayer<-.Assay5" ] }, { "page": "dim.Assay", "title": "Feature and Cell Numbers", "concept": [ "assay" ], "topics": [ "dim.Assay" ] }, { "page": "dim.Assay5", "title": "Feature and Cell Numbers", "concept": [ "assay5" ], "topics": [ "dim.Assay5" ] }, { "page": "dim.DimReduc", "title": "Dimensional Reduction Meta-Information", "concept": [ "dimreduc" ], "topics": [ "dim.DimReduc", "dimnames.DimReduc", "length.DimReduc", "names.DimReduc" ] }, { "page": "dim.Seurat", "title": "Feature and Cell Numbers", "concept": [ "seurat" ], "topics": [ "dim.Seurat" ] }, { "page": "dimnames.Assay", "title": "Assay-Level Feature and Cell Names", "concept": [ "assay", "dimnames" ], "topics": [ "dimnames.Assay", "dimnames<-.Assay" ] }, { "page": "dimnames.Assay5", "title": "Assay-Level Feature and Cell Names", "concept": [ "assay5", "dimnames" ], "topics": [ "dimnames.Assay5", "dimnames<-.Assay5" ] }, { "page": "dimnames.Seurat", "title": "Feature and Cell Names", "concept": [ "dimnames", "seurat" ], "topics": [ "dimnames.Seurat", "dimnames<-.Seurat" ] }, { "page": "DimReduc-class", "title": "The Dimensional Reduction Class", "concept": [ "dimreduc" ], "topics": [ "DimReduc", "DimReduc-class" ] }, { "page": "DimReduc-validity", "title": "Dimensional Reduction Validity", "concept": [ "dimreduc" ], "topics": [ "DimReduc-validity" ] }, { "page": "Distances", "title": "Get the Neighbor nearest neighbors distance matrix", "concept": [ "data-access" ], "topics": [ "Distances", "Distances.Neighbor" ] }, { "page": "droplevels.LogMap", "title": "Drop Unused Logical Map Values", "concept": [ "logmap" ], "topics": [ "droplevels.LogMap" ] }, { "page": "Embeddings", "title": "Get Cell Embeddings", "concept": [ "data-access" ], "topics": [ "Embeddings", "Embeddings.DimReduc", "Embeddings.Seurat" ] }, { "page": "EmptyMatrix", "title": "Empty Matrices", "concept": [ "utils" ], "topics": [ "EmptyMatrix" ] }, { "page": "FetchData", "title": "Access cellular data", "concept": [ "data-access" ], "topics": [ "FetchData", "FetchData.DimReduc", "FetchData.Seurat" ] }, { "page": "FilterObjects", "title": "Find Sub-objects of a Certain Class", "concept": [ "utils" ], "topics": [ "FilterObjects" ] }, { "page": "FOV-class", "title": "The Field of View Object", "concept": [ "fov" ], "topics": [ "FOV", "FOV-class" ] }, { "page": "FOV-methods", "title": "'FOV' Methods", "concept": [ "fov" ], "topics": [ "$.FOV", "Cells.FOV", "Features.FOV", "FetchData.FOV", "FOV-methods", "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" ] }, { "page": "FOV-validity", "title": "FOV Validity", "concept": [ "fov" ], "topics": [ "FOV-validity" ] }, { "page": "GetImage", "title": "Get image data", "concept": [ "data-access" ], "topics": [ "GetImage", "GetImage.Seurat" ] }, { "page": "GetTissueCoordinates", "title": "Get tissue coordinates", "concept": [ "data-access" ], "topics": [ "GetTissueCoordinates", "GetTissueCoordinates.FOV", "GetTissueCoordinates.Seurat" ] }, { "page": "Graph-class", "title": "The Graph Class", "concept": [ "graph" ], "topics": [ "Graph", "Graph-class" ] }, { "page": "VariableFeatures", "title": "Highly Variable Features", "concept": [ "data-access" ], "topics": [ "HVFInfo", "HVFInfo.Assay", "HVFInfo.Assay5", "HVFInfo.Seurat", "SpatiallyVariableFeatures", "SpatiallyVariableFeatures.Assay", "SpatiallyVariableFeatures.Assay5", "SpatiallyVariableFeatures.Seurat", "SVFInfo", "SVFInfo.Assay", "SVFInfo.Assay5", "SVFInfo.Seurat", "SVFInfo.StdAssay", "VariableFeatures", "VariableFeatures.Assay", "VariableFeatures.Assay5", "VariableFeatures.Seurat", "VariableFeatures<-", "VariableFeatures<-.Assay", "VariableFeatures<-.Seurat" ] }, { "page": "Idents", "title": "Get, set, and manipulate an object's identity classes", "concept": [ "seurat" ], "topics": [ "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" ] }, { "page": "Images", "title": "Pull spatial image names", "concept": [ "data-access" ], "topics": [ "Images" ] }, { "page": "NNIndex", "title": "Get Neighbor algorithm index", "concept": [ "data-access" ], "topics": [ "Index", "Index.Neighbor", "Index<-", "Index<-.Neighbor" ] }, { "page": "Indices", "title": "Get Neighbor nearest neighbor index matrices", "concept": [ "data-access" ], "topics": [ "Indices", "Indices.Neighbor" ] }, { "page": "intersect.LogMap", "title": "Find Common Logical Map Values", "concept": [ "logmap" ], "topics": [ "intersect.LogMap" ] }, { "page": "IsGlobal", "title": "Is an object global/persistent?", "concept": [ "data-access" ], "topics": [ "IsGlobal", "IsGlobal.default", "IsGlobal.DimReduc" ] }, { "page": "IsMatrixEmpty", "title": "Check if a matrix is empty", "concept": [ "utils" ], "topics": [ "IsMatrixEmpty", "IsMatrixEmpty.default" ] }, { "page": "IsNamedList", "title": "Check List Names", "concept": [ "utils" ], "topics": [ "IsNamedList" ] }, { "page": "JackStrawData-class", "title": "The JackStrawData Class", "topics": [ "JackStrawData", "JackStrawData-class" ] }, { "page": "JackStrawData-methods", "title": "'JackStrawData' Methods", "concept": [ "jackstraw" ], "topics": [ "$.JackStrawData", ".DollarNames.JackStrawData", "as.logical.JackStrawData", "JackStrawData-methods", "show,JackStrawData-method" ] }, { "page": "SplitLayers", "title": "Split and Join Layers Together", "concept": [ "assay5" ], "topics": [ "JoinLayers", "JoinLayers.Assay5", "JoinLayers.Seurat" ] }, { "page": "JS", "title": "Get and set JackStraw information", "concept": [ "jackstraw" ], "topics": [ "JS", "JS.DimReduc", "JS.JackStrawData", "JS<-", "JS<-.DimReduc", "JS<-.JackStrawData" ] }, { "page": "Key", "title": "Get and set object keys", "concept": [ "data-access" ], "topics": [ "Key", "Key.Assay", "Key.Assay5", "Key.DimReduc", "Key.Seurat", "Key<-", "Key<-.Assay", "Key<-.Assay5", "Key<-.DimReduc", "Keys", "Keys.Seurat" ] }, { "page": "labels.LogMap", "title": "Find Observations by Value", "concept": [ "logmap" ], "topics": [ "labels.LogMap" ] }, { "page": "Layers", "title": "Query and Manipulate Assay Layers", "concept": [ "data-access" ], "topics": [ "LayerData", "LayerData.Assay", "LayerData.Assay5", "LayerData.Seurat", "LayerData<-", "LayerData<-.Assay", "LayerData<-.Assay5", "LayerData<-.Seurat", "Layers", "Layers.Assay", "Layers.Assay5", "Layers.Seurat" ] }, { "page": "Loadings", "title": "Get and set feature loadings", "concept": [ "data-access" ], "topics": [ "Loadings", "Loadings.DimReduc", "Loadings.Seurat", "Loadings<-", "Loadings<-.DimReduc" ] }, { "page": "LogMap-class", "title": "A Logical Map", "concept": [ "logmap" ], "topics": [ "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" ] }, { "page": "LogMap-validity", "title": "Logical Map Validity", "concept": [ "logmap" ], "topics": [ "LogMap-validity" ] }, { "page": "LogSeuratCommand", "title": "Log a command", "concept": [ "command" ], "topics": [ "LogSeuratCommand" ] }, { "page": "merge.Assay", "title": "Merge Assays", "concept": [ "assay" ], "topics": [ "merge.Assay" ] }, { "page": "merge.Assay5", "title": "Merge Assays", "concept": [ "assay5" ], "topics": [ "merge.Assay5" ] }, { "page": "merge.DimReduc", "title": "Merge Dimensional Reductions", "concept": [ "dimreduc" ], "topics": [ "merge.DimReduc" ] }, { "page": "merge.Seurat", "title": "Merge Seurat Objects", "concept": [ "seurat" ], "topics": [ "AddSamples", "merge", "merge.Seurat", "MergeSeurat" ] }, { "page": "Misc", "title": "Get and set miscellaneous data", "concept": [ "data-access" ], "topics": [ "Misc", "Misc.Assay", "Misc.Assay5", "Misc.DimReduc", "Misc.Seurat", "Misc<-", "Misc<-.Assay", "Misc<-.Assay5", "Misc<-.DimReduc", "Misc<-.Seurat" ] }, { "page": "Molecules-class", "title": "The Spatial Molecules Class", "concept": [ "segmentation" ], "topics": [ "Molecules-class" ] }, { "page": "Molecules-methods", "title": "'Molecules' Methods", "concept": [ "segmentation" ], "topics": [ "Features.Molecules", "GetTissueCoordinates.Molecules", "Molecules-methods", "show,Molecules-method", "subset.Molecules" ] }, { "page": "names.Seurat", "title": "Subobject Names", "concept": [ "seurat" ], "topics": [ "names.Seurat" ] }, { "page": "Neighbor-class", "title": "The Neighbor class", "topics": [ "Neighbor", "Neighbor-class" ] }, { "page": "Neighbor-methods", "title": "'Neighbor' Methods", "concept": [ "neighbor" ], "topics": [ "dim.Neighbor", "Neighbor-methods", "show,Neighbor-method" ] }, { "page": "Overlay", "title": "Overlay 'Spatial' Objects Over One Another", "concept": [ "spatial" ], "topics": [ "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" ] }, { "page": "PackageCheck", "title": "Check the existence of a package", "concept": [ "utils" ], "topics": [ "PackageCheck" ] }, { "page": "pbmc_small", "title": "A small example version of the PBMC dataset", "topics": [ "pbmc_small" ] }, { "page": "print.DimReduc", "title": "Print Top Feature Loadings", "concept": [ "dimreduc" ], "topics": [ "print", "print.DimReduc" ] }, { "page": "Project", "title": "Get and set project information", "concept": [ "seurat" ], "topics": [ "Project", "Project.Seurat", "Project<-", "Project<-.Seurat" ] }, { "page": "Radius", "title": "Get the spot radius from an image", "concept": [ "spatialimage" ], "topics": [ "Radius" ] }, { "page": "RandomName", "title": "Generate a random name", "concept": [ "utils" ], "topics": [ "RandomName" ] }, { "page": "RenameAssays", "title": "Rename assays in a 'Seurat' object", "concept": [ "seurat" ], "topics": [ "RenameAssays" ] }, { "page": "RenameCells", "title": "Rename cells", "concept": [ "seurat" ], "topics": [ "RenameCells", "RenameCells.Assay", "RenameCells.Assay5", "RenameCells.DimReduc", "RenameCells.Neighbor", "RenameCells.Seurat" ] }, { "page": "RowMergeSparseMatrices", "title": "Merge Sparse Matrices by Row", "concept": [ "utils" ], "topics": [ "RowMergeSparseMatrices" ] }, { "page": "SaveSeuratRds", "title": "Save and Load 'Seurat' Objects from Rds files", "concept": [ "utils" ], "topics": [ "LoadSeuratRds", "SaveSeuratRds" ] }, { "page": "Segmentation-class", "title": "The 'Segmentation' Class", "concept": [ "segmentation" ], "topics": [ "Segmentation-class" ] }, { "page": "Segmentation-methods", "title": "'Segmentation' Methods", "concept": [ "segmentation" ], "topics": [ "Cells.Segmentation", "coordinates,Segmentation-method", "GetTissueCoordinates.Segmentation", "lengths.Segmentation", "RenameCells.Segmentation", "Segmentation-methods", "show,Segmentation-method", "subset.Segmentation", "[,Segmentation,ANY,ANY,ANY-method", "[[<-,Segmentation,character,missing,ANY-method", "[[<-,Segmentation,character,missing,NULL-method" ] }, { "page": "Segmentation-validity", "title": "Segmentation Validity", "concept": [ "segmentation" ], "topics": [ "Segmentation-validity" ] }, { "page": "set-if-null", "title": "Set If or If Not 'NULL'", "concept": [ "utils" ], "topics": [ "%iff%", "%||%", "set-if-null" ] }, { "page": "Seurat-class", "title": "The Seurat Class", "concept": [ "seurat" ], "topics": [ "Seurat", "Seurat-class" ] }, { "page": "Seurat-validity", "title": "Seurat Object Validity", "concept": [ "seurat" ], "topics": [ "Seurat-validity" ] }, { "page": "SeuratCommand-class", "title": "The 'SeuratCommand' Class", "concept": [ "command" ], "topics": [ "SeuratCommand", "SeuratCommand-class" ] }, { "page": "show-LogMap-method", "title": "'LogMap' Object Overview", "concept": [ "logmap" ], "topics": [ "show,LogMap-method" ] }, { "page": "Simplify", "title": "Simplify Geometry", "concept": [ "spatial" ], "topics": [ "Simplify", "Simplify.Spatial" ] }, { "page": "SpatialImage-class", "title": "The SpatialImage class", "topics": [ "SpatialImage", "SpatialImage-class" ] }, { "page": "SpatialImage-methods", "title": "'SpatialImage' methods", "concept": [ "spatialimage" ], "topics": [ "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" ] }, { "page": "split.Assay", "title": "Split an Assay", "concept": [ "assay" ], "topics": [ "split.Assay" ] }, { "page": "split.Assay5", "title": "Split an Assay", "concept": [ "assay5" ], "topics": [ "split.Assay5" ] }, { "page": "Stdev", "title": "Get the standard deviations for an object", "concept": [ "data-access" ], "topics": [ "Stdev", "Stdev.DimReduc", "Stdev.Seurat" ] }, { "page": "StitchMatrix", "title": "Stitch Matrices Together", "concept": [ "utils" ], "topics": [ "StitchMatrix" ] }, { "page": "subset.Assay", "title": "Subset an Assay", "concept": [ "assay" ], "topics": [ "subset.Assay" ] }, { "page": "subset.Assay5", "title": "Subset an Assay", "concept": [ "assay5" ], "topics": [ "subset.Assay5" ] }, { "page": "subset.DimReduc", "title": "Subset a Dimensional Reduction", "concept": [ "dimreduc" ], "topics": [ "subset.DimReduc" ] }, { "page": "subset.Seurat", "title": "Subset 'Seurat' Objects", "concept": [ "seurat" ], "topics": [ "subset", "subset.Seurat", "[.Seurat" ] }, { "page": "Theta", "title": "Get the offset angle", "concept": [ "spatial" 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