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    Enables evidence-traceable annotation of human and mouse single-cell data by resolving ontology terms, searching versioned marker and reference-atlas indexes, ranking and auditing candidate cell types, and exporting sealed decision bundles with provenance.
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    An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.
    11
    3,713 PyPI
    1
    Apache 2.0
  • A
    license
    A
    quality
    A
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    Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.
    8
    MIT
  • A
    license
    A
    quality
    B
    maintenance
    Enables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.
    4
    MIT
  • A
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    Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.
    24
    38 npm
    2
    MIT
  • A
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    quality
    D
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    Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.
    3
    MIT
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    license
    B
    quality
    B
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    Enables LLM agents to query the CZ CELLxGENE Census single-cell atlas with ontology-aware filters, cost caps, and full provenance, allowing natural language questions about cell types, tissues, and gene expression.
    13
    22 PyPI
    MIT
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    Enables searching and downloading Gene Expression Omnibus (GEO) data from NCBI, including datasets, series, samples, platforms, and profiles, through natural language queries.
    11
    61 PyPI
    17
    BSD 3-Clause
  • A
    license
    B
    quality
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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
    81 PyPI
    44
    MIT
  • A
    license
    B
    quality
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    maintenance
    Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.
    1
    46
    MIT
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    Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.
    9
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  • F
    license
    B
    quality
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    maintenance
    BioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.
    73
    12
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  • A
    license
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    quality
    C
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    An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.
    52
    12
    BSD 3-Clause
  • A
    license
    Not graded
    quality
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    maintenance
    Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.
    10
    MIT
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    Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.
    MIT