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UCE (Universal Cell Embeddings) — species-agnostic cell embedding model from Stanford SNAP Lab that uses protein language models (ESM-2) to create universal cell representations without species-specif
Use with AI
Install the MCP server or CLI to instantly fetch UCE documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/uce
Expression Atlas is the EMBL-EBI database and programmatic toolkit for querying baseline and differential gene expression across thousands of experiments in 50+ species. Use this skill to search exper
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nf-core — community-curated Nextflow pipeline framework with 100+ production bioinformatics pipelines. Provides CLI tools for listing, launching, downloading, creating, and linting pipelines; managing
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Use when working with SATURN for cross-species single-cell RNA-seq integration that combines AnnData count matrices with protein embedding TorchDicts. SATURN trains macrogene representations with k-me
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2 shared topics • 1 shared operation
gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr
2 shared topics • 1 shared operation