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Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering
Use with AI
Install the MCP server or CLI to instantly fetch Seurat documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/seurat
docker pull biocontainers/seurat:unknownscanpy-plots — visualization layer of the Scanpy single-cell RNA-seq analysis suite (scanpy.pl module). Generates UMAP, t-SNE, PCA embeddings, violin plots, dot plots, heatmaps, matrix plots, stacked
3 shared topics • 2 shared operations
scverse — the community-maintained Python ecosystem for single-cell and spatial omics analysis. Coordinates AnnData (universal data structure), scanpy (scRNA-seq QC/clustering/DE), squidpy (spatial tr
3 shared topics • 2 shared operations
SEACells — single-cell metacell identification using kernel archetypal analysis. Aggregates highly similar single cells into metacells that preserve transcriptional and epigenomic heterogeneity while
3 shared topics • 2 shared operations
Pegasus — scalable single-cell RNA-seq analysis toolkit for millions of cells. Command-line tool and Python package for preprocessing, batch correction, clustering, differential expression, visualizat
2 shared topics • 3 shared operations
scDblFinder — Bioconductor R package for detecting doublets in single-cell RNA-seq data using simulation-based classification with gradient boosting. Identifies neotypic and heterotypic doublets in dr
2 shared topics • 3 shared operations