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Use when working with GSVA (Gene Set Variation Analysis) for sample-wise gene set enrichment scoring from RNA-seq or microarray expression data. GSVA computes continuous enrichment scores per sample u
Use with AI
Install the MCP server or CLI to instantly fetch GSVA documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gsva
10x Genomics — commercial platform for single-cell and spatial genomics assays including Chromium single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq, single-cell multiome (RNA+ATAC), Visium spatial
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Use when working with Conos (Clustering On Network Of Samples), the R package for joint analysis of multiple single-cell RNA-seq and spatial transcriptomics datasets. Covers building joint k-nearest-n
3 shared topics
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
Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering
3 shared topics
STdeconvolve — reference-free cell-type deconvolution for spatial transcriptomics using Latent Dirichlet Allocation (LDA). Decomposes multi-cellular spatial pixels into cell-type proportions and trans
3 shared topics