satijalab/seurat

Health v2 · maintenance only

Flags: no_license

Adoption not part of the score

2790 stars · 995 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

Seurat is an R toolkit for single-cell genomics developed by the Satija Lab, providing a complete pipeline for analyzing single-cell RNA-seq, multimodal, and spatially-resolved transcriptomics data. Version 5 adds scalable analysis methods, cross-modality integration via bridge integration, sketch-based workflows for millions of cells, and spatial dataset support.

Use cases

• analyze single-cell rna-seq data in r
• cluster and visualize single cell gene expression
• integrate scrna-seq and scatac-seq datasets
• analyze spatial transcriptomics data like visium
• run differential expression on single cell clusters
• map query cells onto a multimodal reference atlas
• scale single cell analysis to millions of cells
• demultiplex hashed samples with hashtag oligos

When to choose

• you work in R and need a mature, well-documented single-cell analysis pipeline
• you need multimodal or cross-modality integration (RNA + ATAC, protein, spatial)
• you need to analyze very large datasets with sketch-based or on-disk (BPCells) workflows
• you want extensive tutorials, vignettes, and an active community for scRNA-seq analysis

When to avoid

• you need a Python-based single-cell workflow (consider Scanpy instead)
• you need raw sequencing processing or alignment rather than downstream analysis
• you need a non-genomics data analysis toolkit
• you cannot install R (version 4.0+) or its compiled dependencies

Facets

library · maturity stable

data-science machine-learning data-visualization nlp bioinformatics data-science machine-learning windows single-cell-genomics scrna-seq spatial-transcriptomics multimodal-analysis data-integration clustering dimensionality-reduction differential-expression r-package cran bioconductor-adjacent human-cell-atlas scatac-seq reference-mapping sketch-based-analysis macos linux r

Member repositories

For agents

markdown · JSON · MCP: product_card(name="satijalab/seurat")