The Seurat object is a representation of single-cell expression data for R;
each Seurat object revolves around a set of cells and consists of one or more
Assay objects, or individual representations of
expression data (eg. RNA-seq, ATAC-seq, etc). These assays can be reduced
from their high-dimensional state to a lower-dimension state and stored as
DimReduc objects. Seurat objects also
store additional metadata, both at the cell and feature level (contained
within individual assays). The object was designed to be as self-contained as
possible, and easily extendable to new methods.
assaysA list of assays for this project
meta.dataContains meta-information about each cell, starting with
number of features detected (nFeature) and the original identity class
(orig.ident); more information is added using AddMetaData
active.assayName of the active, or default, assay; settable using
DefaultAssay
active.identThe active cluster identity for this Seurat object;
settable using Idents
graphsA list of Graph objects
neighbors...
reductionsA list of dimensional reduction objects for this object
imagesA list of spatial image objects
project.nameName of the project
miscA list of miscellaneous information
versionVersion of Seurat this object was built under
commandsA list of logged commands run on this Seurat object
toolsA list of miscellaneous data generated by other tools, should be
filled by developers only using Tool<-
Seurat object, validity, and interaction methods
$.Seurat(),
Seurat-validity,
[[.Seurat(),
[[<-,Seurat,
[[<-,Seurat,NULL,
dim.Seurat(),
dimnames.Seurat(),
merge.Seurat(),
names.Seurat(),
subset.Seurat()