Seurat-class: The Seurat Class
In lambdamoses/SeuratBasics: Slimmed down version of Seurat

Description Slots

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.

assays: A list of assays for this project
meta.data: Contains 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.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-class objects
neighbors: ...
reductions: A list of dimmensional reduction objects for this object
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<-