"All items" matching MCP servers:

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

Enables AI agents to resolve scientific names to Taxonomic Serial Numbers, traverse complete taxonomic lineages from kingdom to children, and retrieve vernacular names in all languages from an authoritative US-government taxonomy.

Enables searching cancer genes and curated variants from CIViC, retrieving associated diseases, therapies, and graded evidence items and assertions for clinical interpretation.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

Enables LLM agents to search EMDB cryo-EM maps, look up UniProt proteins, compute ESM-2 sequence embeddings, retrieve cryo-EM maps from a protein sequence via a two-tower model, and search GEO DNA-methylation arrays, all through typed tools with structured output. Ships with a 40-question evaluation harness that runs Claude as the MCP client.

Enables citation-grounded biomedical literature review by searching PubMed, retrieving abstracts from Europe PMC, and looking up gene and protein records from NCBI Gene and UniProt, with every cited PMID verified to exist and support its claim. All tools are read-only, so Claude can only cite papers actually retrieved and read during the session.

Predicts CRISPR gene dependencies and drug targets by integrating literature, regulatory/PPI networks, and genome-scale metabolic models.

Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.

Enables Claude and other MCP clients to run fast, exactly scored similarity and substructure searches over a local PubChem fingerprint index, pull live PubChem records (identifiers, synonyms, GHS, bioassays) with cited sources, and compute offline RDKit descriptors, med-chem alerts and highlighted structure drawings — all without API rate limits.

Exposes five local tools that let AI agents quantify Western blots, IHC/stain and immunofluorescence colocalization images, and analyze or independently verify qPCR data. Paths are restricted to configured allow-listed directories, so all computation stays on the user's machine.