Seurat
Overview
Seurat is an R package and data object for single-cell genomics, developed and maintained by the Satija Lab at the New York Genome Center. First described in 2015 (Satija et al., Nature Biotechnology), it is widely used for single-cell RNA-seq analysis in the R ecosystem. The Seurat object is the central data structure: it stores a cell-by-feature count matrix together with cell metadata, dimensionality reductions, cluster assignments, and multi-modal assay layers in a single in-memory object. Seurat v5 extended support to spatially resolved transcriptomics (Visium, Xenium, MERFISH) and introduced sketch-based analysis for datasets spanning millions of cells. In the R ecosystem, Seurat occupies a role analogous to AnnData in the Python scverse ecosystem. The two can be converted via interoperability packages, with AnnData’s h5ad format serving as the common exchange format between them.
Connections
- Upstream source: count matrices from SAM-BAM-CRAM alignment and quantification
- Interoperable with: AnnData (h5ad as common exchange format)
- Annotations use: Cell Ontology (cell types), UBERON (anatomy)
Resources
- https://satijalab.org/seurat/
- https://github.com/satijalab/seurat
- https://doi.org/10.1038/nbt.3192 (Satija et al. 2015, Nature Biotechnology — original paper)
- https://doi.org/10.1038/s41587-023-01767-y (Hao et al. 2023, Nature Biotechnology — Seurat v5)