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Seurat Developer's Guide

Seurat is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. Centered around the Seurat object, Seurat enables This guide is to help developers understand how the Seurat object is structured, how to interact with the object and access data from it, and how to develop new methods for Seurat objects.

Semantics

Throughout all Seurat-related documentation and writing, the following styles for distinguishing between Seurat objects, as well as any associated objects, and Seurat will and be used. For Seurat objects, or the object within R, the word 'Seurat' will always be written in monospaced text. When referring to the package Seurat, it will always be written in normal text. Both Seurat and Seurat will be always capitalized. This style will be used throughout documentation for Seurat as well as any vignettes and tutorials produced by the authors.

Object Overview

The center of all Seurat analyses is the Seurat object. The Seurat object serves as a collection of Assay and DimReduc objects, representing expression data and a dimensionality reduction of expression data, respectively. The Assay objects are designed to hold expression data from a single experiment, such as RNAseq gene expression, CITE-seq ADTs, cell hashtags, or imputed gene values. Each Seurat object can hold any combination of Assays, allowing for a wide variety of multi-modal analyses.