Satija R, Hoffman P, Hao Y, Hartman A, Molla G, Butler A, Stuart T (2023). +
Hoffman P, Satija R, Collins D, Hao Y, Hartman A, Molla G, Butler A, Stuart T (2024). SeuratObject: Data Structures for Single Cell Data. -R package version 5.0.1, -https://github.com/mojaveazure/seurat-object, https://mojaveazure.github.io/seurat-object/. +R package version 5.0.2, +https://github.com/satijalab/seurat-object, https://satijalab.github.io/seurat-object/.
@Manual{,
title = {SeuratObject: Data Structures for Single Cell Data},
- author = {Rahul Satija and Paul Hoffman and Yuhan Hao and Austin Hartman and Gesmira Molla and Andrew Butler and Tim Stuart},
- year = {2023},
- note = {R package version 5.0.1,
-https://github.com/mojaveazure/seurat-object},
- url = {https://mojaveazure.github.io/seurat-object/},
+ author = {Paul Hoffman and Rahul Satija and David Collins and Yuhan Hao and Austin Hartman and Gesmira Molla and Andrew Butler and Tim Stuart},
+ year = {2024},
+ note = {R package version 5.0.2,
+https://github.com/satijalab/seurat-object},
+ url = {https://satijalab.github.io/seurat-object/},
}
%||% from rlang (#178)UpdateSeuratObject (@ddiez, #182)... to call signature for Radius generic (#190)PolyVtx (#194)UpdateSeuratObject to run without Seurat installed (#199)Layers.Assay() when the search returns no results (@maxim-h, #189)subset to allow empty images to be dropped (#204)GetAssayData() to use layer instead of slot (#160)SaveSeuratRds() to move all layers instead of just those in tempdir() (#169)SetAssayData() to use layer instead of slot (#171)FilterObjects() to .FilterObjects() (#171)GetAssayData() to use layer instead of slot (#160)SaveSeuratRds() to move all layers instead of just those in tempdir() (#169)SetAssayData() to use layer instead of slot (#171)FilterObjects() to .FilterObjects() (#171)head and tail methods for Seurat and Assay objects (#5)head and tail methods for Seurat and Assay objects (#5)AttachDeps to attach required imported dependencies on package attachmentAssay objects to replace Seurat::SCTAssay or Signac::ChromatinAssay objects of the same namedata.table/tibble objects (#4)NULL if a subset results in zero cells (#9)Assay objects to replace Seurat::SCTAssay or Signac::ChromatinAssay objects of the same namedata.table/tibble objects (#4)NULL if a subset results in zero cells (#9)R/assay5.R
+ Source: R/assay5.R
AddMetaData-StdAssay.RdR/generics.R, R/assay.R, R/assay5.R, and 1 more
+ Source: R/generics.R, R/assay.R, R/assay5.R, and 1 more
AddMetaData.RdR/generics.R, R/seurat.R, R/assay.R
+ Source: R/generics.R, R/seurat.R, R/assay.R
AssayData.RdR/generics.R, R/fov.R
+ Source: R/generics.R, R/fov.R
Boundaries.RdR/generics.R, R/assay5.R
+ Source: R/generics.R, R/assay5.R
CastAssay.RdR/generics.R, R/default.R, R/assay5.R, and 2 more
+ Source: R/generics.R, R/default.R, R/assay5.R, and 2 more
Cells.Rddimnames.Assay5(),
-dimnames.Assay(),
+
dimnames.Assay(),
+dimnames.Assay5(),
dimnames.Seurat()
R/seurat.R
+ Source: R/seurat.R
CellsByIdentities.RdR/seurat.R
+ Source: R/seurat.R
CellsByImage.RdCentroids MethodsR/generics.R, R/utils.R
+ Source: R/generics.R, R/utils.R
CheckMatrix.RdR/generics.R, R/fov.R
+ Source: R/generics.R, R/fov.R
CreateFOV.RdMolecules ObjectR/generics.R, R/molecules.R
+ Source: R/generics.R, R/molecules.R
CreateMolecules.RdSegmentation ObjectsR/generics.R, R/segmentation.R
+ Source: R/generics.R, R/segmentation.R
CreateSegmentation.RdSeurat objectR/generics.R, R/seurat.R
+ Source: R/generics.R, R/seurat.R
CreateSeuratObject.RdR/generics.R, R/graph.R, R/assay.R, and 4 more
+ Source: R/generics.R, R/graph.R, R/assay.R, and 4 more
DefaultAssay.RdR/generics.R, R/seurat.R
+ Source: R/generics.R, R/seurat.R
DefaultFOV.RdR/generics.R, R/assay.R, R/assay5.R
+ Source: R/generics.R, R/assay.R, R/assay5.R
DefaultLayer.RdR/generics.R, R/neighbor.R
+ Source: R/generics.R, R/neighbor.R
Distances.RdR/generics.R, R/dimreduc.R, R/seurat.R
+ Source: R/generics.R, R/dimreduc.R, R/seurat.R
Embeddings.RdCreate empty 0x0 matrices of varying types
+EmptyMatrix(repr = "C", type = "d")Representation of empty matrix; choose from:
“C” for a
+ CsparseMatrix
“T” for a
+ TsparseMatrix
“R” for an
+ RsparseMatrix
“e” for an
+ unpackedMatrix
“d” for a dense S3 matrix
“spam” for a spam matrix
Type of resulting matrix to return, choose from:
“d” for numeric matrices
“l” for logical matrices
“n” for pattern matrices
Note, when repr is “spam”, type must be
+“d”; when repr is “d”, setting type
+to “n” returns a logical matrix
A 0x0 matrix of the specified representation and type
+EmptyMatrix()
+#> 0 x 0 sparse Matrix of class "dgCMatrix"
+#> <0 x 0 matrix>
+EmptyMatrix("spam")
+#> <0 x 0 matrix>
+#> Class 'spam' (32-bit)
+
+FOV MethodsR/generics.R, R/seurat.R
+ Source: R/generics.R, R/seurat.R
GetTissueCoordinates.RdR/generics.R, R/seurat.R
+ Source: R/generics.R, R/seurat.R
Idents.RdR/generics.R, R/neighbor.R
+ Source: R/generics.R, R/neighbor.R
Indices.RdR/generics.R, R/default.R, R/dimreduc.R
+ Source: R/generics.R, R/default.R, R/dimreduc.R
IsGlobal.RdR/generics.R, R/utils.R
+ Source: R/generics.R, R/utils.R
IsMatrixEmpty.RdWhether or not x is empty
R/generics.R, R/jackstraw.R, R/dimreduc.R
+ Source: R/generics.R, R/jackstraw.R, R/dimreduc.R
JS.RdR/generics.R, R/assay.R, R/assay5.R, and 2 more
+ Source: R/generics.R, R/assay.R, R/assay5.R, and 2 more
Key.RdR/generics.R, R/assay.R, R/assay5.R, and 1 more
+ Source: R/generics.R, R/assay.R, R/assay5.R, and 1 more
Layers.RdR/generics.R, R/dimreduc.R, R/seurat.R
+ Source: R/generics.R, R/dimreduc.R, R/seurat.R
Loadings.RdR/generics.R, R/assay.R, R/assay5.R, and 2 more
+ Source: R/generics.R, R/assay.R, R/assay5.R, and 2 more
Misc.Rd.DataA list of SpatialPoints objects
A list of SpatialPoints objects
keyR/generics.R, R/neighbor.R
+ Source: R/generics.R, R/neighbor.R
NNIndex.Rdv+f9~&hZ~6mNH#-
zTPITw4%+TJkQpThbGkun1ZS*OBFMG`ST}o$=8X(?su(J*O`5nZ(!3?vsHN~;0