Immunology and Microbiology

Installable Claude components for immune-repertoire analysis, epitope prediction, antibody design, microbial genomics, metagenomics, and host-pathogen interaction modelling.

10x Genomics Cloud MCP

MCP server · 10x Genomics · GA

Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.

K-Dense skill that submits designed protein and antibody sequences to the Adaptyv cloud lab for wet-lab binding, expression, thermostability, and activity assays, with NetSolP/SoluProt/SolubleMPNN/ESM/ipTM/pSAE pre-screening.

AlphaFold MCP Server

MCP server · Augmented Nature · GA

MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.

AnnData (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill teaching the AnnData annotated-data-matrix format used by Scanpy and scvi-tools for single-cell and other observation/feature matrices.

Anthropic PubMed Connector

MCP server · Anthropic · GA

Anthropic-managed NCBI literature search via PubMed and PubMed Central.

BGPT Paper Search (Claude Skill)

Claude Skill · K-Dense · GA

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.

Bakta (Claude Skill)

Claude Skill · SciAgent · GA

Annotate bacterial and archaeal genomes and plasmids with Bakta’s Prodigal/HMM/diamond pipeline.

BioContextAI Knowledgebase MCP

MCP server · BioContextAI · GA

Read-only MCP that unifies 14+ biomedical databases (Antibody Registry, UniProt, STRING, AlphaFold, KEGG, Open Targets) for immune and protein-context queries.

BioMCP

MCP server · GenomOncology · GA

Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.

BioPython (Claude Skill)

Claude Skill · K-Dense · GA

Comprehensive molecular biology toolkit.

BioRender Connector

MCP server · BioRender · GA

Scientific-figure assembly from the 50,000+ BioRender icon and template library.

BioServices (Claude Skill)

Claude Skill · K-Dense · GA

Unified Python interface to 40+ bioinformatics services.

Biomni (Claude Skill)

Claude Skill · Stanford SNAP Lab · GA

General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.

CellChat (Claude Skill)

Claude Skill · SciAgent · GA

Infer and visualize intercellular communication from scRNA-seq with CellChat (R).

Cellxgene Census (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for querying the CZ CELLxGENE Discover census — 50M+ standardized single-cell observations across 1,000+ datasets via TileDB-SOMA, with AnnData / Scanpy integration.

Composer

Plugin · Scripps AI Enablement · Beta

Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and recommending autonomous systems.

Consensus Plugin

Claude Code Plugin · Consensus · GA

Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.

Database Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.

ETE Toolkit (Claude Skill)

Claude Skill · K-Dense · GA

Phylogenetic tree toolkit (ETE).

Ensembl MCP Server

MCP server · effieklimi · GA

MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.

FlowIO (Claude Skill)

Claude Skill · K-Dense · GA

Skill that parses Flow Cytometry Standard (FCS v2–3.1) files into NumPy/pandas for immunophenotyping pipelines and metadata extraction.

Glycoengineering (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for protein-glycosylation analysis — N-glycosylation sequon scanning, O-glycosylation hotspot prediction, and access to NetOGlyc/GlycoShield/GlycoWorkbench for therapeutic antibody and vaccine design.

Human Protein Atlas MCP Server

MCP server · Augmented Nature · GA

Query the Human Protein Atlas — tissue/blood/brain expression, subcellular localization, cancer markers, and antibody validation/staining data.

Hypothesis Generation (Claude Skill)

Claude Skill · K-Dense · GA

Structured hypothesis formulation from observations.

LIANA-MCP

MCP server · scmcphub · GA

MCP server wrapping LIANA so Claude can infer and plot cell-cell communication from single-cell data in natural language.

Literature Review (Claude Skill)

Claude Skill · K-Dense · GA

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).

Paper Lookup (Claude Skill)

Claude Skill · K-Dense · GA

Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.

Phylogenetics (Claude Skill)

Claude Skill · K-Dense · GA

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML).

Prokka (Claude Skill)

Claude Skill · SciAgent · GA

Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka’s BLAST/HMM pipeline.

PyDESeq2 (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill for bulk RNA-seq differential expression with PyDESeq2 — size factors, dispersion, Wald / LRT testing, BH-adjusted p-values.

Roary (Claude Skill)

Claude Skill · SciAgent · GA

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary’s CD-HIT + BLAST + MCL clustering pipeline.

Scanpy-MCP

MCP server · scmcphub · GA

MCP server wrapping Scanpy so Claude can run end-to-end single-cell RNA-seq analyses (QC, clustering, DE, plotting) from natural language.

Scholar Gateway Connector (Wiley)

MCP server · Wiley · Beta

Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.

Scientific Brainstorming (Claude Skill)

Claude Skill · K-Dense · GA

Creative research ideation and exploration.

Scientific Critical Thinking (Claude Skill)

Claude Skill · K-Dense · GA

Evaluate scientific claims and evidence quality.

Synapse.org Connector

MCP server · Sage Bionetworks · GA

Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.

ToolUniverse

MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA

Harvard / MIT MCP server bundling 600+ vetted scientific tools — literature, chemistry, omics, clinical trials — for AI-scientist-style hypothesis exploration.

UniProt MCP Server

MCP server · Augmented Nature · GA

MCP server giving Claude 26 tools over the UniProt REST API for protein search, domains, orthologs, PTMs, pathways, and multi-format export.

bio-research (Claude Code Plugin)

Claude Code Plugin · Anthropic · GA

Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.

decoupler-MCP

MCP server · scmcphub · GA

MCP server wrapping decoupler so Claude can infer pathway and transcription-factor activities from expression data in natural language.

gget (Claude Skill)

Claude Skill · K-Dense · GA

Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.