{ "_id": "6a227c79cd65a98ecbd4ed85", "Package": "SeuratObject", "Type": "Package", "Title": "Data Structures for Single Cell Data", "Version": "4.1.4", "Authors@R": "c(\nperson(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),\nperson(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),\nperson(given = 'Paul', family = 'Hoffman', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),\nperson(given = 'Tim', family = 'Stuart', email = 'tstuart@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),\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'),\nperson(given = \"Yuhan\", family = \"Hao\", email = 'yhao@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-1810-0822'))\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) for more\ndetails.", "URL": "https://mojaveazure.github.io/seurat-object/,\nhttps://github.com/mojaveazure/seurat-object", "BugReports": "https://github.com/mojaveazure/seurat-object/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "Collate": "'RcppExports.R' 'zzz.R' 'generics.R' 'graph.R' 'assay.R'\n'centroids.R' 'command.R' 'data.R' 'default.R' 'jackstraw.R'\n'dimreduc.R' 'segmentation.R' 'keymixin.R' 'molecules.R'\n'spatial.R' 'fov.R' 'logmap.R' 'neighbor.R' 'seurat.R'\n'utils.R'", "Config/Needs/website": "pkgdown", "Repository": "https://satijalab.r-universe.dev", "Date/Publication": "2023-09-27 20:12:08 UTC", "RemoteUrl": "https://github.com/satijalab/seurat-object", "RemoteRef": "v4.1.4", "RemoteSha": "9788970c5789134cdf30d60b2a72d814f9304a84", "NeedsCompilation": "yes", "Packaged": { 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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": "IsGlobal", "title": "Is an object global/persistent?", "concept": [ "data-access" ], "topics": [ "IsGlobal", "IsGlobal.default", "IsGlobal.DimReduc" ] }, { "page": "IsMatrixEmpty", "title": "Check if a matrix is 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"concept": [ "data-access" ], "topics": [ "Loadings", "Loadings.DimReduc", "Loadings.Seurat", "Loadings<-", "Loadings<-.DimReduc" ] }, { "page": "LogMap-class", "title": "A Logical Map", "topics": [ "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" ] }, { "page": "LogSeuratCommand", "title": "Log a command", "concept": [ "command" ], "topics": [ "LogSeuratCommand" ] }, { "page": "MatchCells", "title": "Match Cells", "topics": [ "MatchCells", "MatchCells.character", "MatchCells.NULL", "MatchCells.numeric" ] }, { "page": "Misc", "title": "Get and set miscellaneous data", "concept": [ "data-access" ], "topics": [ "Misc", "Misc.Assay", "Misc.DimReduc", "Misc.Seurat", "Misc<-", "Misc<-.Assay", "Misc<-.DimReduc", "Misc<-.Seurat" ] }, { "page": "Molecules-class", "title": "The Spatial Molecules Class", "concept": [ "segmentation" ], "topics": [ "Molecules-class" ] }, { "page": "Molecules-methods", "title": "'Molecules' Methods", "topics": [ "Features.Molecules", "GetTissueCoordinates.Molecules", "Molecules-methods", "show,Molecules-method", "subset.Molecules" ] }, { "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", "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": "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.DimReduc", "RenameCells.Neighbor", "RenameCells.Seurat" ] }, { "page": "RowMergeSparseMatrices", "title": "Merge Sparse Matrices by Row", "concept": [ "utils" ], "topics": [ "RowMergeSparseMatrices" ] }, { "page": "s4list", "title": "S4/List Conversion", "concept": [ "utils" ], "topics": [ "IsS4List", "ListToS4", "s4list", "S4ToList", "S4ToList.default", "S4ToList.list" ] }, { "page": "Segmentation-class", "title": "The 'Segmentation' Class", "concept": [ "segmentation" ], "topics": [ "Segmentation-class" ] }, { "page": "Segmentation-methods", "title": "'Segmentation' Methods", "concept": [ "future" ], "topics": [ "Cells.Segmentation", "coordinates,Segmentation-method", "GetTissueCoordinates.Segmentation", "lengths.Segmentation", "RenameCells.Segmentation", "Segmentation-methods", "show,Segmentation-method", "subset.Segmentation", "[,Segmentation,ANY,ANY,ANY-method" ] }, { "page": "set-if-na", "title": "Set if 'NA'", "concept": [ "utils" ], "topics": [ "%!NA%", "%!na%", "%NA%", "%na%", "set-if-na" ] }, { "page": "Seurat-class", "title": "The Seurat Class", "topics": [ "Seurat", 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