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-class
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-class objects. Seurat objects also store additional
meta data, both at the cell and feature level (contained within individual assays). The
object was designed to be as self-contained as possible, and easily extendible to new methods.
assaysA list of assays for this project
meta.dataContains meta-information about each cell, starting with number of genes detected (nGene)
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-class objects
neighbors...
reductionsA list of dimmensional reduction objects for this object
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<-