Contents
What does a Seurat object contain?
The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single-cell dataset. For a technical discussion of the Seurat object structure, check out our GitHub Wiki. For example, the count matrix is stored in pbmc[[“RNA”]]@counts .
What is Seurat used for?
Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
What is BCR Sequencing?
B-cell receptor (BCR) sequencing offers an important approach for examining immune responses to infection. Antigen-specific BCRs are often sequenced following single-cell sorting with antigen baits. However, this strategy is low throughput.
Is CITE-seq quantitative?
CITE-seq uses DNA-barcoded antibodies to convert detection of proteins into a quantitative, sequenceable readout.
What kind of information is stored in a Seurat file?
It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This vignette serves as a guide to saving and loading Seurat objects to h5Seurat files.
What does data loaded mean in Seurat vignette?
The data loaded is the raw, unprocessed version of the data. In order to generate the full dataset, we’ll follow the steps outlined in Seurat’s spatial dataset vignette. As seen, we have a dataset with multiple components to it.
What makes a R6 object an object in Seurat?
Unlike most R objects (called S3 and S4), and more like objects in Python, R6 objects are objects; this means that methods are attached directly to the object instead of to a generic function. In Seurat, most functions take an object as input and return an object as output.
How to save an object in h5seurat file?
Saving an object is as simple as calling SaveH5Seurat; minimally, this function takes a Seurat object and nothing else. Optional arguments are present for specifying a filename and whether or not you want to overwrite a preexisting file.