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    Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.
    77
    MIT
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    MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.
    11
    MIT
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    Enables AI assistants to query the eggNOG 7 database in natural language for protein lookups, orthologous groups, pairwise orthologs, protein families, taxonomy, and database statistics. Also delivers structured functional annotations such as KEGG KO and GO terms with confidence scores, plus an index of bulk-downloadable data files.
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    1
    MIT
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    Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.
    20
    162 PyPI
    45
    MIT
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    Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.
    414 npm
    MIT
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    Provides AI assistants with access to microbial type strain genome data, including species information, 16S rDNA sequences, functional annotations, statistics, and citation/usage guidance.
    1
    MIT
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    Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.
    339 npm
    MIT
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    Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.
    381 npm
    3
    Apache 2.0
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    Enables LLMs to search, retrieve, and analyze Global Catalogue of Metagenomics data—including BioProjects, BioSamples, Runs, MAGs, biome catalogues, taxonomy abundance, functional annotations, and platform statistics—through natural-language MCP tools.
    1
    MIT
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    Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.
    383 npm
    MIT
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    Enables querying BindingDB for measured protein/small-molecule binding affinities, including finding ligands that bind a protein, protein targets for a compound, and affinities from PDB structures.
    430 npm
    MIT
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    A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.
    42 PyPI
    MIT
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    A professional MCP server for comprehensive bioinformatics quality control, providing automated FastQC/MultiQC analysis, HTML report parsing, and advanced data visualization for sequencing data.
    1
    MIT
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    Provides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.
    2
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    An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.
    15
    MIT
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    Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.
    11
    MIT
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    Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.
    9
    MIT
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    Enables AI assistants to search ImmPort immunology studies and subjects, read study data and assay results, look up controlled vocabularies and the data model, and find study files. Supports study comparison, release history lookups, and guided workflows for cross-study analysis.
    9
    MIT
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    Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.
    5
    Apache 2.0
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    Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.
    2
    126 PyPI
    MIT
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    Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.
    17
    MIT
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    Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.
    9
    MIT