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 · verified: degraded · security: caution
Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.
AMR / Resistome Detection (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Profile the antimicrobial-resistance gene content (resistome) of shotgun metagenomes with RGI, AMR++/MEGARes, deepARG, and AMRFinderPlus/ABRicate
Adaptyv (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
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 · verified: works · security: caution
MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.
Amplicon Processing (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Convert demultiplexed 16S/ITS amplicon FASTQs into exact amplicon sequence variants (ASVs) with DADA2 — primer removal, per-run error modeling, pair merging and chimera removal
AnnData (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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 · verified: works · security: cleared
Anthropic-managed NCBI literature search via PubMed and PubMed Central.
Antibody Registry (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Persistent antibody identifiers (RRIDs) and vendor/catalog metadata from the Antibody Registry; a source in the Research Resources connector in Claude Science.
BGPT Paper Search (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
BLAST (Bio-MCP)
MCP server · Bio-MCP · GA · verified: works · security: caution
MCP server wrapping NCBI BLAST+ for nucleotide/protein similarity search and custom database creation, run locally over stdio.
Bakta (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Annotate bacterial and archaeal genomes and plasmids with Bakta’s Prodigal/HMM/diamond pipeline.
BioContextAI Knowledgebase MCP
MCP server · BioContextAI · GA · verified: works · security: cleared
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 · verified: degraded · security: cleared
Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.
BioPython (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Comprehensive molecular biology toolkit.
BioRender Connector
MCP server · BioRender · GA · verified: degraded · security: cleared
Scientific-figure assembly from the 50,000+ BioRender icon and template library.
BioServices (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Unified Python interface to 40+ bioinformatics services.
Biomni (Claude Skill)
Claude Skill · Stanford SNAP Lab · GA · verified: works · security: caution
General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.
Blatant-Why (BY) Protein Design Agent
Claude Code Plugin · 001TMF · Beta · verified: works · security: caution
Scaffolds a Claude Code antibody and nanobody design campaign — 19 skills, 13 slash commands, and 11 MCP servers wired to design models and cloud compute.
Boltz (Claude Code Plugin)
Claude Code Plugin · Boltz · GA · verified: works · security: caution
Skills that drive the hosted Boltz API to predict biomolecular structures, screen and design small molecules, and design protein/antibody binders.
CAN-IMMUNE
MCP server · Li/Purcell Lab, Monash University · GA · verified: works · security: caution
Hosted MCP server over the CAN-IMMUNE cancer neoantigen database — mutant peptides, cell lines, tissues, and MHC-I binding predictions.
CELLxGENE CellGuide (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Cell-type reference cards (markers, ontology, descriptions) from CZ CELLxGENE CellGuide; the CellGuide connector in Claude Science.
CellChat (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Infer and visualize intercellular communication from scRNA-seq with CellChat (R).
Cellxgene Census (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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.
Clustering and Phenotyping (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Unsupervised cell-type discovery in high-dimensional cytometry with FlowSOM, PhenoGraph and CATALYST — type-vs-state markers, over-provision then metacluster, UMAP for display only
Compensation and Transformation (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Corrects fluorophore spillover or spectral overlap and applies logicle/arcsinh transforms — spillover-matrix estimation, AutoSpill, and cofactor choice for CyTOF vs fluorescence
Composer
Plugin · Scripps AI Enablement · Beta · verified: works · security: cleared
Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and, for open-ended goals, assembling a multi-agent system from those same components.
Consensus Plugin
Claude Code Plugin · Consensus · GA · verified: degraded · security: cleared
Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.
Cytometry Differential Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Tests cytometry clusters for differential abundance and differential state with diffcyt — sample-as-unit aggregation, design/contrast matrices, compositionality checks, BH FDR
Cytometry QC (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Cleans flow, spectral and mass cytometry acquisitions — margin removal, time-based anomaly detection with flowAI/PeacoQC/flowCut, dead-cell and CyTOF checks, batch outlier flagging
Database Lookup (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.
Differential Abundance (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Test which microbiome taxa differ between groups using compositionally-aware methods (ALDEx2, ANCOM-BC2, MaAsLin, LinDA, ZicoSeq) and report a multi-tool consensus
EMBL-EBI OLS (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Resolve and navigate biomedical ontology terms (GO, MONDO, HP, CHEBI, CL, UBERON, EFO, …) across 250+ ontologies via the EMBL-EBI Ontology Lookup Service.
ETE Toolkit (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Phylogenetic tree toolkit (ETE).
Ensembl MCP Server
MCP server · effieklimi · GA · verified: works · security: cleared
MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.
Epitope Prediction (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Predict B-cell and T-cell epitopes for vaccine and epitope-mapping work with BepiPred-3.0, DiscoTope-3.0, the IEDB tools, and MHC presentation predictors
FlowIO (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Skill that parses Flow Cytometry Standard (FCS v2–3.1) files into NumPy/pandas for immunophenotyping pipelines and metadata extraction.
Functional Profiling (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Profile metagenome functional potential with HUMAnN 3 tiered search, producing species-stratified gene-family and MetaCyc pathway abundances with normalization guidance
Gating Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Defines cytometry populations with manual or automated gates — hierarchical GatingSets, openCyto templates, flowDensity thresholds, and FlowJo round-tripping via CytoML
Gene Ontology MCP Server
MCP server · Augmented Nature · Beta · verified: works · security: caution
Query GO terms, annotations, and enrichment inputs from the Gene Ontology; part of the Genes & Ontologies connector in Claude Science.
GlyGen MCP Server
MCP server · GlyGen · Beta · verified: degraded · security: caution
First-party remote MCP server over GlyGen’s integrated glycan, glycoprotein, biomarker, and disease data — protein, site, glycan, biomarker, and disease summaries.
Glycoengineering (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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 · verified: works · security: caution
Query the Human Protein Atlas — tissue/blood/brain expression, subcellular localization, cancer markers, and antibody validation/staining data.
Hypothesis Crucible (Claude Plugin)
Claude Plugin · Scripps AI Enablement · GA · verified: works · security: cleared
Agentic cross-corpus hypothesis generation — mines typed knowledge fragments from literature, structured databases, and raw experimental data, bridges them Swanson-style into novel connections, then runs a falsification gauntlet that aggressively rejects non-novel, ungrounded, contradicted, or implausible ideas, emitting only survivors with cited support and a discriminating experimental test.
Hypothesis Generation (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Structured hypothesis formulation from observations.
Immcantation BCR Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Reconstruct B-cell clonal families, quantify somatic hypermutation and selection, and build antibody lineage trees from AIRR-seq data with the Immcantation R suite
Immunogenicity Scoring (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Rank neoantigen and epitope candidates by likely T-cell response using NeoFox features, PRIME2.0, BigMHC-IM, the fitness model and pVACtools tiering
Immunotherapy Response Prediction (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that predicts immune-checkpoint-inhibitor response by integrating TMB, MSI, PD-L1, HLA, and immune gene expression into a 0–100 score.
Interface Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Map protein-protein and protein-ligand interfaces with Bio.PDB — contact residues, buried surface area, and telling a real interface from crystal packing
Kraken2 Metagenomic Classification (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Classify shotgun metagenomic reads to taxa with Kraken2 minimizer/LCA matching, then re-estimate abundance with Bracken
LIANA-MCP
MCP server · scmcphub · GA · verified: works · security: caution
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 · verified: works · security: cleared
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
MGnify (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Microbiome/metagenomics analyses, taxonomy, and functional profiles from EMBL-EBI’s MGnify; a source in the Omics Archives connector in Claude Science.
MHC Binding Prediction (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes
MHC Class II Prediction (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Predict peptide-MHC class II (HLA-DR/DQ/DP) binding for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0, with the reliability caveats class II demands
MetaPhlAn Profiling (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Profile shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4 clade-specific markers, with cell-fraction vs read-fraction and index-pinning guidance
MiXCR Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Align V(D)J reads and assemble TCR/BCR clonotypes with MiXCR, driven by a chemistry-matched preset, exporting native or AIRR TSV for downstream repertoire analysis
MyGene.info MCP (BioThings)
MCP server · longevity-genie · GA · verified: works · security: cleared
Gene annotation and ID conversion across species via MyGene.info/BioThings; the Genes & Ontologies connector in Claude Science.
Neoantigen Prediction (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Identify tumor neoantigens from somatic variants with pVACtools for personalized cancer vaccines and checkpoint biomarkers, centering clonality, HLA LOH, expression, and validation tiers
Ontology Lookup Service (OLS) MCP Server
MCP server · seandavi · Beta · verified: works · security: caution
Search and resolve terms across hundreds of biomedical ontologies via EMBL-EBI’s OLS; part of the Genes & Ontologies connector in Claude Science.
PBMCpedia MCP
MCP server · MCPmed · Beta · verified: works · security: caution
Query PBMCpedia’s harmonized PBMC single-cell atlas — per-cell-type expression, DEGs, pathways and antibody chains — filtered by sex, age and disease.
Paper Lookup (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.
Phylogenetics (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
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 · verified: works · security: cleared
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka’s BLAST/HMM pipeline.
Proto-OKN MCP Server
MCP server · SBL-SDSC (San Diego Supercomputer Center) · Beta · verified: works · security: cleared
Natural-language access to 30+ NSF Proto-OKN scientific knowledge graphs (SPOKE biomedicine, BioBricks chemical safety, more) via SPARQL, schema inspection, and cross-graph bridging.
PyDESeq2 (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill for bulk RNA-seq differential expression with PyDESeq2 — size factors, dispersion, Wald / LRT testing, BH-adjusted p-values.
Repertoire Visualization (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Render TCR/BCR repertoire figures — V-J chord diagrams, spectratypes, clonal tracking, rarefaction curves, overlap heatmaps and similarity networks — with depth-robust metric guidance
Revvity Signals AI Connector
Claude.ai Connector · Revvity Signals Software · GA · verified: degraded · security: cleared
Claude.ai connector giving natural-language access to the Revvity Signals electronic lab notebook and connected R&D data.
Roary (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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 · verified: works · security: caution
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 · verified: works · security: cleared
Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.
Scientific Brainstorming (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Creative research ideation and exploration.
Scientific Critical Thinking (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Evaluate scientific claims and evidence quality.
Seqera MCP
MCP server · Seqera Labs · GA · verified: works · security: cleared
Hosted MCP server for launching and managing Nextflow/nf-core pipelines on the Seqera Platform and retrieving public SRA/ENA/GEO sequencing data.
Specificity Annotation (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Annotate TCR/BCR sequences against antigen-specificity databases and cluster by shared-specificity signal, treating matches as hypotheses with generation-probability nulls
Strain Tracking (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Resolve and compare bacterial strains below species level from shotgun metagenomes using inStrain popANI, StrainPhlAn, MIDAS2, StrainGE and skani/fastANI
Synapse.org Connector
MCP server · Sage Bionetworks · GA · verified: works · security: cleared
Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.
TCR-Epitope Binding (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Infer or annotate TCR antigen specificity via unsupervised clustering (tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), with honest caveats on supervised prediction
Taxonomy Assignment (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Assign taxonomy to 16S/ITS/18S amplicon ASVs using DADA2, DECIPHER IDTAXA or QIIME2 classifiers against SILVA/GTDB/Greengenes2/UNITE, with region-specific training guidance
ToolUniverse
MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA · verified: works · security: cleared
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 · verified: works · security: caution
MCP server giving Claude 26 tools over the UniProt REST API for protein search, domains, orthologs, PTMs, pathways, and multi-format export.
VDJtools Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Compute depth-normalized TCR/BCR repertoire diversity (Hill profiles), overlap, clonality and segment usage with VDJtools/immunarch, with estimator and normalization guidance
arXiv MCP Server
MCP server · blazickjp · GA · verified: works · security: cleared
Search and retrieve arXiv preprints (incl. q-bio) and metadata; part of the Literature Graph connector in Claude Science.
bio-research (Claude Code Plugin)
Claude Code Plugin · Anthropic · GA · verified: degraded · security: cleared
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 · verified: works · security: caution
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 · verified: works · security: cleared
Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.
instrument-data-to-allotrope
Claude Skill · Anthropic · GA · verified: works · security: cleared
Converts 40+ lab-instrument output formats to Allotrope Simple Model JSON / CSV for LIMS and data-lake ingestion.
nextflow-development
Claude Skill · Anthropic · GA · verified: works · security: cleared
Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.
scGPT (Claude Skill)
Claude Skill · Bo Wang Lab, University of Toronto · GA · verified: works · security: cleared
scGPT single-cell foundation model for cell-type annotation, integration, and perturbation prediction; runs locally as a Claude Science skill.
scientific-problem-selection
Claude Skill · Anthropic · GA · verified: works · security: caution
Structured framework for research project ideation, risk assessment, and troubleshooting, based on Fischbach & Walsh (Cell 2024).
scikit-bio (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Skill for microbiome ecology — reads BIOM/FASTA, computes alpha/beta diversity (UniFrac), PCoA, PERMANOVA, and builds phylogenetic trees.
scirpy Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Integrate single-cell paired TCR/BCR repertoires with gene expression using scirpy — chain-pairing QC, clonotype definition, clonal expansion, diversity, and VDJdb specificity
scvi-tools
Claude Skill · Anthropic · GA · verified: works · security: cleared
Deep-learning workflows for scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, and related scvi-tools models for single-cell omics.
single-cell-rna-qc
Claude Skill · Anthropic · GA · verified: works · security: cleared
scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.
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