R: The Seurat Class

Seurat-class {SeuratObject} | R Documentation

## The Seurat Class

### Description

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.

### Slots

`assays`

  A list of assays for this project

`meta.data`

  Contains 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.assay`

  Name of the active, or default, assay; settable using `DefaultAssay`

`active.ident`

  The active cluster identity for this Seurat object; settable using `Idents`

`graphs`

  A list of `Graph` objects

`neighbors`

  ...

`reductions`

  A list of dimensional reduction objects for this object

`images`

  A list of spatial image objects

`project.name`

  Name of the project

`misc`

  A list of miscellaneous information

`version`

  Version of Seurat this object was built under

`commands`

  A list of logged commands run on this `Seurat` object

`tools`

  A list of miscellaneous data generated by other tools, should be filled by developers only using `Tool<-`

[Package SeuratObject version 4.0.3 Index]