All tools

Every catalogued component, one page each. Use the sidebar (or the search box at the top of the page) to jump to a specific tool. To browse by research area instead, see the Catalog index.

GlyGen MCP Server - First-party remote MCP server over GlyGen's integrated glycan, glycoprotein, biomarker, and disease data — protein, site, glycan, biomarker, and disease summaries.
LabMate MCP - One-install cheminformatics MCP with 81 tools — retrosynthesis, forward/ADMET/pKa/NMR prediction, 202 named reactions, reagent calculators, compound and literature lookup.
Proto-OKN MCP Server - 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.
AlphaGenome Single-Variant Analysis (Claude Skill) - Predict non-coding variant effects on expression, chromatin accessibility, histone marks, splicing, and TF binding via the AlphaGenome API.
Drug Repurposing (Claude Skill) - ToolUniverse agent skill that finds drug-repurposing candidates via target-, compound-, and disease-driven strategies with mechanism and feasibility scoring.
Foldseek Structural Search (Claude Skill) - Submit a 3D protein structure (.pdb/.cif) and find structurally similar proteins across AFDB, PDB100, SwissProt, and more via the Foldseek API.
GTEx Expression Database (Claude Skill) - Query the GTEx Portal for median RNA expression (TPM) across 54 human tissues and eQTLs linking variants to gene expression.
UniBind TF Binding Sites (Claude Skill) - Query UniBind for experimentally validated transcription-factor binding sites; download BED/FASTA coordinates by species, cell line, or TF.
10x Genomics Cloud MCP - Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.
A/B Compartment Analysis (bioSkills) - Call A/B chromatin compartments from balanced Hi-C matrices with cooltools eigendecomposition, phased against GC or gene density so the A sign is not arbitrary
ABCD Study Pipeline (Claude Skill) - End-to-end workflow for the ABCD Study dataset, including download via NIMH Data Archive, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI
ABIDE Pipeline (Claude Skill) - End-to-end workflow for the ABIDE (Autism Brain Imaging Data Exchange) dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data
ACMG Classification (bioSkills) - Classifies germline variants P/LP/VUS/LB/B under ACMG-AMP 2015 with ClinGen SVI specifications, Tavtigian Bayesian points, and calibrated in-silico thresholds
ADHD-200 Pipeline (Claude Skill) - End-to-end workflow for the ADHD-200 dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data
ADMET Prediction (ToolUniverse Claude Skill) - ToolUniverse agent skill that profiles a compound's absorption, distribution, metabolism, excretion, and toxicity into a graded pass/warn/fail scorecard.
ADMETlab MCP Server - Self-hostable MCP server wrapping the ADMETlab 3.0 API for molecule washing, SVG rendering, ADMET property prediction, and CSV retrieval.
ADNI Pipeline (Claude Skill) - End-to-end workflow for ADNI data (fMRI + T1), including BIDS preparation, fMRIPrep preprocessing, and DK68 ROI pipeline.
AIBL Pipeline (Claude Skill) - End-to-end workflow for the AIBL (Australian Imaging, Biomarkers and Lifestyle) dataset, including data access guidance, BIDS organization, and multimodal processing of sMRI and PET …
AIND Data MCP - Official Allen Institute MCP server giving Claude query and NWB-introspection access to AIND's V2 neuroscience data assets.
ALKYL - Claude Code plugin bundling 27 computational-chemistry skills — RDKit, docking, MD, quantum chemistry, free energy, generative design — plus four keyless MCP servers.
AMR / Resistome Detection (bioSkills) - Profile the antimicrobial-resistance gene content (resistome) of shotgun metagenomes with RGI, AMR++/MEGARes, deepARG, and AMRFinderPlus/ABRicate
AOMIC Pipeline (Claude Skill) - End-to-end workflow for the AOMIC (Amsterdam Open MRI Collection) dataset, including data access, BIDS organization, and multimodal processing of sMRI, rs-fMRI, and task-fMRI
ARCHS4 (Claude Skill) - Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples.
ASL Perfusion MRI (Claude Skill) - Process Arterial Spin Labeling (ASL) perfusion MRI data including CBF (cerebral blood flow) quantification, ASL preprocessing (motion correction, partial volume correction, M0 normalization), or …
AWS HealthLake MCP Server - Apache-2.0 MCP server for AWS HealthLake FHIR datastores — CRUD, advanced search, patient-everything, and import/export jobs, with a read-only safety mode.
Adaptive Designs (bioSkills) - Plan group-sequential, sample-size re-estimation, seamless Phase 2/3 and enrichment trials with rpact/gsDesign, against FDA and ICH E20 adaptive-design guidance
Adaptyv (Claude Skill) - 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.
AdisInsight Plugin - Springer Nature AdisInsight MCP plugin surfacing drug-development pipeline, clinical-trial, and deal intelligence to Claude for repurposing and competitive scouting.
Adverse Event Detection (ToolUniverse Claude Skill) - ToolUniverse agent skill that detects adverse-drug-event signals from FDA FAERS with disproportionality statistics (PRR, ROR, IC) and a 0–100 safety signal score.
Adverse Outcome Pathway (ToolUniverse Claude Skill) - ToolUniverse agent skill that maps chemicals to adverse outcome pathways using AOPWiki, GHS/IARC classification, LD50 data, and toxicogenomics.
Aging and Senescence Research (ToolUniverse Claude Skill) - ToolUniverse agent skill for geroscience — senescence markers, aging hallmarks, longevity GWAS, and senolytic target discovery with graded evidence.
Alignment Trimming (bioSkills) - Trim multiple sequence alignments with ClipKIT, trimAl, BMGE, Divvier or HMMcleaner, choosing the mode by downstream goal rather than by habit
AlphaFold MCP Server - MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.
AlphaFold2 (Claude Skill) - AlphaFold2 protein/complex structure prediction, run locally or via a hosted API with an optional ColabFold MSA server; a Claude Science skill.
Amplicon Processing (bioSkills) - 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 teaching the AnnData annotated-data-matrix format used by Scanpy and scvi-tools for single-cell and other observation/feature matrices.
Anthropic PubMed Connector - Anthropic-managed NCBI literature search via PubMed and PubMed Central.
Antibody Registry (Claude Science Connector) - Persistent antibody identifiers (RRIDs) and vendor/catalog metadata from the Antibody Registry; a source in the Research Resources connector in Claude Science.
Arboreto (Claude Skill) - Claude skill for gene-regulatory-network inference with Arboreto — GRNBoost2 / GENIE3 tree-based regression over bulk or single-cell expression, distributed via Dask.
ArrayExpress / BioStudies MCP Server - Search functional-genomics studies and metadata in ArrayExpress/BioStudies; part of the Omics Archives connector in Claude Science.
Astropy (Claude Skill) - Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology.
AutoDock Vina (Claude Skill) - Molecular docking with AutoDock Vina (Python API).
Autoskill (Claude Skill) - Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain …
BCFtools (Claude Skill) - CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats.
BCI-MCP - MCP server streaming live EEG brain-state metrics (focus, calm, attention, band powers) from OpenBCI/Muse/LSL devices — or a hardware-free synthetic mode — into Claude.
BEDTools (Claude Skill) - Genomic interval ops on BED/BAM/GFF/VCF.
BGPT Paper Search (Claude Skill) - Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
BIDS (Claude Skill) - Claude skill for organizing, validating, and querying Brain Imaging Data Structure datasets — MRI, EEG, MEG, iEEG, PET, microscopy, behavioral, and 35 BIDS entities.
BLAST (Bio-MCP) - MCP server wrapping NCBI BLAST+ for nucleotide/protein similarity search and custom database creation, run locally over stdio.
BOLD5000 Pipeline (Claude Skill) - End-to-end workflow for the BOLD5000 dataset, including download, BIDS organization, and processing of task-fMRI data with visual image stimuli
BRENDA (Claude Skill) - BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data.
BWA-MEM2 (Claude Skill) - Fast short-read DNA aligner for WGS/WES/ChIP-seq.
Bakta (Claude Skill) - Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline.
Bayesian Trials (bioSkills) - Design Bayesian dose-finding, basket and platform trials with RBesT MAP priors, BOIN/CRM escalation and EXNEX borrowing, against current FDA Bayesian guidance
Benchling (Claude Skill) - Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.
Binder Discovery (ToolUniverse Claude Skill) - ToolUniverse agent skill that discovers small-molecule binders for a target via known-ligand mining, similarity expansion, docking, and ADMET filtering into a ranked shortlist.
Binding Site Detection (bioSkills) - Find and rank druggable pockets on an apo protein with fpocket, P2Rank, CASTp and DoGSiteScorer — including cryptic pockets over an MD ensemble
BindingDB (Claude Science Connector) - Measured protein–small-molecule binding affinities from BindingDB; a source in the Chemistry connector in Claude Science.
BioBank Japan (Claude Science Connector) - East Asian biobank GWAS summary statistics from BioBank Japan (PheWeb); a source in the Human Genetics connector in Claude Science.
BioContextAI Knowledgebase MCP - Read-only MCP that unifies 14+ biomedical databases (Antibody Registry, UniProt, STRING, AlphaFold, KEGG, Open Targets) for immune and protein-context queries.
BioMCP - Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.
BioMart (Claude Science Connector) - Bulk biological data-mining and ID mapping via Ensembl BioMart; the BioMart connector in Claude Science.
BioPython (Claude Skill) - Comprehensive molecular biology toolkit.
BioRender Connector - Scientific-figure assembly from the 50,000+ BioRender icon and template library.
BioServices (Claude Skill) - Unified Python interface to 40+ bioinformatics services.
Biomni (Claude Skill) - 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 - 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) - Skills that drive the hosted Boltz API to predict biomolecular structures, screen and design small molecules, and design protein/antibody binders.
Borzoi (Claude Skill) - Borzoi sequence-to-expression model predicting RNA-seq coverage from DNA sequence; runs locally as a Claude Science skill.
Brain Visualization (Claude Skill) - Visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors
BrainGNN (Claude Skill) - Run BrainGNN for fMRI phenotype prediction, including graph construction, training, and evaluation.
BrainNetworkTransformer (BNT) (Claude Skill) - Run BrainNetworkTransformer for fMRI phenotype prediction, including data loading, training, and evaluation.
Brian2 (Claude Skill) - Build spiking neural network simulations in Brian2 — equation-based neuron models, synaptic plasticity, monitors, and multicompartment morphology.
Bulk RNA-seq (Claude Skill) - End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a …
CAN-IMMUNE - Hosted MCP server over the CAN-IMMUNE cancer neoantigen database — mutant peptides, cell lines, tissues, and MHC-I binding predictions.
CDISC Data Handling (bioSkills) - Read SDTM XPT files, derive ADaM datasets with traceability, apply TEAE conventions, and validate for FDA submission with Pinnacle 21 or CORE
CDXML Toolkit - MCP server that draws molecules and reaction schemes to publication-ready ChemDraw CDXML, parses ELN/LCMS/NMR files, and reads structures from images.
CELLxGENE CellGuide (Claude Science Connector) - Cell-type reference cards (markers, ontology, descriptions) from CZ CELLxGENE CellGuide; the CellGuide connector in Claude Science.
CIViC (Claude Science Connector) - Crowd-curated clinical interpretations of cancer variants from CIViC (WashU); a source in the Clinical Genomics connector in Claude Science.
CMS Coverage MCP (Anthropic Healthcare) - Anthropic-published MCP server over the CMS Coverage Database — Local and National Coverage Determinations for Medicare prior-auth, appeals, and policy lookup.
CMS data.gov MCP Server - MIT-licensed MCP server over data.cms.gov — search, query, and export CMS public datasets (provider enrollment, hospital quality, spending) for healthcare analytics.
CNV Inference (bioSkills) - Infer chromosome-scale copy-number alterations from tumor scRNA-seq to separate malignant from normal cells and call subclones with inferCNV, copyKAT, Numbat and SCEVAN
CNVkit (Claude Skill) - Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).
COBRApy (Claude Skill) - Claude skill driving COBRApy for constraint-based metabolic modelling — FBA, FVA, gene knockouts, flux sampling, gapfilling on SBML genome-scale models.
COBRE Pipeline (Claude Skill) - End-to-end workflow for the COBRE dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data for schizophrenia research
CONN Toolbox (Claude Skill) - Perform advanced functional connectivity (ROI-to-ROI, seed-to-voxel, ICA) or effective connectivity (PPI, gPPI, DCM) analysis using the CONN Toolbox
COSMIC (Claude Skill) - Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.
Calcium Imaging Analysis Guide (Claude Skill) - Decide motion correction, ROI extraction, neuropil correction, dF/F and spike inference for two-photon and miniscope calcium imaging
Cam-CAN Pipeline (Claude Skill) - End-to-end workflow for the Cam-CAN (Cambridge Centre for Ageing and Neuroscience) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, task-fMRI, and MEG, phenotype …
Cancer Genomics TCGA (ToolUniverse Claude Skill) - ToolUniverse agent skill for TCGA/GDC cancer genomics — cohort construction, clinical metadata, somatic mutation frequencies, CNV, survival analysis, and OncoKB variant interpretation.
Cancer Variant Interpretation (ToolUniverse Claude Skill) - ToolUniverse agent skill that turns a gene + somatic variant + cancer type into an evidence-graded precision-oncology report with therapies, resistance, and matching trials.
Cell Line Profiling (ToolUniverse Claude Skill) - ToolUniverse agent skill that ranks cancer cell lines for an experiment by cross-referencing DepMap, Cellosaurus, COSMIC, and PharmacoDB.
CellChat (Claude Skill) - Infer and visualize intercellular communication from scRNA-seq with CellChat (R).
CellRank-MCP - MCP server wrapping CellRank so Claude can model cell fate and trajectories from single-cell data in natural language.
CellTypist (Claude Skill) - Automated scRNA-seq cell type annotation via pre-trained logistic regression.
Cellpose (Claude Skill) - DL cell/nucleus segmentation for fluorescence and brightfield microscopy.
Cellxgene Census (Claude Skill) - 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.
Certus Drug Information MCP Server - MIT openFDA MCP server focused on drug shortages, recalls, labels, and adverse events — with a zero-install hosted endpoint and batch analysis across up to 25 drugs.
ChEBI (Claude Science Connector) - Chemical Entities of Biological Interest — curated small-molecule ontology and annotations; a source in the Chemistry connector in Claude Science.
ChEMBL Connector - Anthropic-packaged plugin and Claude.ai connector over EMBL-EBI's ChEMBL bioactive-compound database — compound, target, bioactivity, and mechanism-of-action lookup.
Chai-1 (Claude Skill) - Chai-1 biomolecular structure prediction (proteins, nucleic acids, ligands) run locally or via a hosted server; a Claude Science skill.
ChatSpatial - MCP server for spatial transcriptomics — preprocessing, spatial domains, deconvolution, cell-cell communication, and SVG detection via Scanpy/Squidpy.
ChemCP - MCP App that renders interactive 2D molecular structures from SMILES and computes basic properties inside Claude conversations via RDKit.js.
ChemGraph - Argonne MCP server that runs real molecular simulations through ASE — geometry optimization, energies, and frequencies via xTB, DFT, or ML potentials.
ChemLint - MCP server exposing 150+ molecular machine-learning tools — SMILES cleaning, descriptors, similarity, clustering, model training — so Claude runs cheminformatics ML without Python scripting.
Chemical Safety (ToolUniverse Claude Skill) - ToolUniverse agent skill for chemical hazard and toxicology assessment via ADMET-AI, CTD toxicogenomics, AOPWiki, GHS/IARC classification, and regulatory safety data.
Chemical Sourcing (ToolUniverse Claude Skill) - ToolUniverse agent skill that finds commercial suppliers for a compound across ZINC, Enamine, eMolecules, and Mcule, with purchasable-analog fallback.
ChimeraX MCP Server - Drive UCSF ChimeraX from Claude in natural language — open, mutate, visualize, measure, and render protein structures; ChimeraX auto-launches.
Chromatin Loop Calling (bioSkills) - Call focal chromatin loops from Hi-C or Micro-C maps with cooltools dots, chromosight and Mustache, and validate them with aggregate peak analysis
Cirq (Claude Skill) - Google quantum computing framework.
Citation Management (Claude Skill) - Comprehensive citation management for academic research.
Clair Variant Caller (Claude Skill) - Agent skill for the Clair suite — germline, somatic, mosaic, and long-read RNA variant calling with Clair3/ClairS/Clair-Mosaic.
ClinGen (Claude Science Connector) - Expert-curated gene–disease validity and variant clinical significance from ClinGen; a source in the Clinical Genomics connector in Claude Science.
ClinPGx (PharmGKB) (Claude Skill) - Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations …
ClinVar (Claude Skill) - Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations.
Clinical Decision Support (Claude Skill) - Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports …
Clinical Note Extract (Anthropic Healthcare Plugin) - Anthropic Claude skill that extracts structured, validated records from unstructured clinical notes with span-level provenance and explicit null handling.
Clinical Reports (Claude Skill) - Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries).
Clinical Trial Design (ToolUniverse Claude Skill) - ToolUniverse agent skill that scores trial feasibility across endpoint, population, comparator, effect size, duration, and regulatory pathway using precedent trials.
Clinical Trial Matching (ToolUniverse Claude Skill) - ToolUniverse agent skill that turns a molecular profile into ranked trial matches across ClinicalTrials.gov, EU CTIS, and ISRCTN with evidence tiers.
ClinicalTrials.gov MCP Server (cyanheads) - Apache-2.0 MCP server over the ClinicalTrials.gov v2 API — trial search, full study records, outcomes / adverse-event extraction, and patient-to-trial matching. Hosted public instance available.
Clustering and Phenotyping (bioSkills) - 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
Com-BrainTF (Claude Skill) - Run Com-BrainTF (Community-aware Brain Transformer) for fMRI phenotype prediction.
Compensation and Transformation (bioSkills) - Corrects fluorophore spillover or spectral overlap and applies logicle/arcsinh transforms — spillover-matrix estimation, AutoSpill, and cofactor choice for CyTOF vs fluorescence
Complex Portal (Claude Science Connector) - Curated macromolecular complexes from EMBL-EBI's Complex Portal; a source in the Structures & Interactions connector in Claude Science.
Composer - 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.
Consciousness Council (Claude Skill) - Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge.
Consensus Plugin - Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.
Cortellis Plugin - Clarivate Cortellis MCP plugin surfacing global drug-pipeline, clinical-trial, regulatory, safety, and deals intelligence to Claude for competitive scouting and regulatory work.
CovaSyn Chemistry MCP - Hosted deterministic cheminformatics MCP with 130+ tools spanning ADMET, docking, retrosynthesis, ICH M7 toxicology, NMR/MS, and biologics design.
Covariation Analysis (bioSkills) - Test whether a proposed RNA secondary structure is actually supported by evolutionary covariation, using R-scape and an explicit statistical-power check
Cytometry Differential Analysis (bioSkills) - 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) - 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
DDInter (Claude Skill) - Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs).
DESeq2 (R/Bioconductor) (Claude Skill) - Bulk RNA-seq DE with R/Bioconductor DESeq2.
DIPY (Claude Skill) - Execute concrete DIPY operations: load DWI (NIfTI+bvals+bvecs), optional masking, DTI fitting, compute FA/MD/AD/RD, and extract ROI statistics.
DMT-HAR-MED Pipeline (Claude Skill) - End-to-end workflow for the DMT-HAR-MED dataset (ds006644), including download, BIDS organization, and processing of rs-fMRI data from a psychedelic intervention study
DNAnexus (Claude Skill) - DNAnexus cloud genomics platform.
DOCX (Claude Skill) - The user wants to create, read, edit, or manipulate Word documents (.docx files).
DailyMed (Claude Skill) - Query FDA drug labels (DailyMed) via REST API.
Dask (Claude Skill) - Distributed computing for larger-than-RAM pandas/NumPy workflows.
Database Lookup (Claude Skill) - Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.
Datamol (Claude Skill) - Claude skill wrapping Datamol — an RDKit-based Python library for molecular standardization, transformations, featurization, and parallel processing on large compound libraries.
DeepChem (Claude Skill) - Claude skill driving DeepChem for molecular machine learning — graph neural nets (GCN, GAT, MPNN, AttentiveFP), featurization, and the MoleculeNet benchmarks (toxicity, ADMET, quantum properties).
DeepLabCut (Claude Skill) - Run markerless animal pose estimation with DeepLabCut — project setup, keypoint labeling, training, SuperAnimal models, and 2D/3D behavioral tracking
DepMap (Claude Skill) - Claude skill for querying the Cancer Dependency Map — CRISPR Chronos gene-effect scores, PRISM drug sensitivity, mutation, expression, and CN data across cancer cell lines.
Dictionary Learning (rs-fMRI) (Claude Skill) - Perform resting-state network decomposition using DictLearning.
DiffDock (Claude Skill) - Claude skill driving DiffDock, a diffusion-based deep-learning docker that predicts protein–ligand binding poses from PDB plus SMILES with per-pose confidence scores.
Differential Abundance (bioSkills) - Test which microbiome taxa differ between groups using compositionally-aware methods (ALDEx2, ANCOM-BC2, MaAsLin, LinDA, ZicoSeq) and report a multi-tool consensus
Diffusion MRI (DWI) (Claude Skill) - Preprocess diffusion MRI / DWI data, compute diffusion metrics (FA/MD/AD/RD, etc.), extract ROI-wise diffusion features, or run tractography/connectome-related workflows
Dose-Response Analysis (ToolUniverse Claude Skill) - ToolUniverse agent skill that fits four-parameter logistic curves to concentration-response data, returning IC50/EC50, Hill slope, Emax, and fit quality.
Doublet Detection (bioSkills) - Flag and remove droplets containing two or more cells in single-cell RNA-seq using scDblFinder, Scrublet and DoubletFinder before clustering
Drift-Diffusion Model (Claude Skill) - Select, fit and validate drift-diffusion models of two-choice reaction-time data using HDDM, PyDDM, fast-dm or EZ-diffusion
Drug Mechanism Research (ToolUniverse Claude Skill) - ToolUniverse agent skill that traces a drug's mechanism from primary target through off-targets, pathways, FDA label, and pharmacogenomics.
Drug Pipeline MCP Server - MCP server aggregating clinical trials, FDA/EMA approvals, safety data, and labels into source-traceable drug pipeline intelligence — no predictions, every output cites its primary source.
Drug Regulatory Research (ToolUniverse Claude Skill) - ToolUniverse agent skill for jurisdiction-aware approval status — UNII identity, ATC/EPC class, Orange Book patents and exclusivity, generic availability, label parsing.
Drug Research (ToolUniverse Claude Skill) - ToolUniverse agent skill that compiles a comprehensive drug dossier — mechanism, targets, ADMET, trials, FAERS safety, pharmacogenomics, and approval history.
Drug Synergy (ToolUniverse Claude Skill) - ToolUniverse agent skill that quantifies drug-combination synergy using Bliss, HSA, Loewe, ZIP, and Chou-Talalay reference models.
Drug Target Validation (ToolUniverse Claude Skill) - ToolUniverse agent skill that scores a drug target 0–100 across genetic, druggability, safety, and clinical-precedent gates with a GO/NO-GO recommendation.
Drug-Drug Interaction (ToolUniverse Claude Skill) - ToolUniverse agent skill that assesses drug-drug interactions via CYP/transporter pharmacokinetics, pharmacodynamic overlap, and 0-100 clinical risk scoring.
DrugBank MCP Server - Community MCP server exposing a local DrugBank SQLite (17k+ drugs) with 16 query methods for repurposing, target lookup, interactions, and structural similarity.
EEG Processing (Claude Skill) - Load, preprocess, epoch, filter, or extract features from EEG data (resting-state, task-based, BCI, clinical, motor imagery, emotion, epilepsy, fatigue, etc.)
EMBL-EBI OLS (Claude Skill) - Resolve and navigate biomedical ontology terms (GO, MONDO, HP, CHEBI, CL, UBERON, EFO, …) across 250+ ontologies via the EMBL-EBI Ontology Lookup Service.
EMDB (Claude Skill) - Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS.
ENA (Claude Skill) - ENA REST API for sequences, reads, assemblies, and annotations.
ENCODE (Claude Skill) - ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types.
ENCODE Toolkit - MCP server + Claude Code plugin for the ENCODE Project: search/download functional-genomics data and run ChIP/ATAC/RNA-seq/Hi-C/WGBS/CUT&RUN pipelines.
ESM (Claude Skill) - Comprehensive toolkit for EvolutionaryScale protein language models including ESM3 (generative multimodal design across sequence, structure, and function) and ESM C (efficient embeddings).
ESMFold (Claude Skill) - ESMFold single-sequence protein structure prediction (no MSA), run locally or via the ESM Atlas API; a Claude Science skill.
ETE Toolkit (Claude Skill) - Phylogenetic tree toolkit (ETE).
Effect Measures (bioSkills) - Compute OR, RR, RD, HR and NNT with calibrated confidence intervals, and report marginal versus conditional estimands per FDA 2023 covariate-adjustment guidance
Ensembl MCP Server - MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.
Enzyme Kinetics (ToolUniverse Claude Skill) - ToolUniverse agent skill that fits Michaelis-Menten kinetics to substrate-velocity data and classifies inhibition mechanism with a Ki estimate.
Epitope Prediction (bioSkills) - 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
Evo 2 (Claude Skill) - Evo 2 genome language model for DNA/RNA/protein sequence generation and variant scoring; local (Hopper GPU) or NVIDIA-hosted; a Claude Science skill.
Exa Search (Claude Skill) - Web toolkit powered by Exa, tuned for scientific and technical content.
Exploratory Data Analysis (Claude Skill) - Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
FDA MCP Server (OpenPharma) - MIT MCP server over the FDA Orange Book, Purple Book, and openFDA — patent-cliff forecasting, therapeutic equivalents, and biosimilar interchangeability.
FM-APP (Claude Skill) - Run FM-APP for phenotype prediction using fMRI ROI features and optional sMRI features.
FSL (Claude Skill) - Process neuroimaging data with FSL (FMRIB Software Library), covering structural MRI, functional MRI (fMRI), and diffusion MRI (dMRI/DTI)
FinnGen (Claude Science Connector) - Finnish biobank GWAS summary statistics across thousands of endpoints from FinnGen; a source in the Human Genetics connector in Claude Science.
FlowIO (Claude Skill) - Skill that parses Flow Cytometry Standard (FCS v2–3.1) files into NumPy/pandas for immunophenotyping pipelines and metadata extraction.
FluidSim (Claude Skill) - Framework for computational fluid dynamics simulations using Python.
Fraud Detection (Anthropic Healthcare Plugin) - Anthropic Claude skill that screens Medicare/Medicaid claims for fraud, waste, and abuse, producing ranked, fully-cited investigation referrals for SIU teams.
FreeSurfer (Claude Skill) - Process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline
Functional Profiling (bioSkills) - Profile metagenome functional potential with HUMAnN 3 tiered search, producing species-stratified gene-family and MetaCyc pathway abundances with normalization guidance
GATK (Claude Skill) - GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs.
GLM (Task-fMRI) (Claude Skill) - Run a classical General Linear Model (GLM) for task-evoked fMRI activation analysis.
GPCR Structural Pharmacology (ToolUniverse Claude Skill) - ToolUniverse agent skill for GPCR drug discovery — ligand classification, GPCRdb structures, mutation effects, and antibody-antigen interface analysis.
GROMACS MCP Server - Run GROMACS molecular-dynamics simulations and trajectory analysis from Claude via a Docker container with GROMACS 2025.4 pre-installed.
GSEApy (Claude Skill) - GSEA and over-representation analysis (ORA) for RNA-seq and proteomics.
GWAS Catalog (Claude Skill) - NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS.
GWAS Drug Discovery (ToolUniverse Claude Skill) - ToolUniverse agent skill that turns GWAS-significant loci into druggable targets and repurposing candidates via fine-mapping, tractability scoring, and drug matching.
GWAS-MCP - Single-install MCP server exposing 30+ tools across 14 biological databases (UniProt, Ensembl, ClinVar, GWAS Catalog, STRING, AlphaFold, KEGG, Open Targets, OMIM) for variant-to-target research.
Gating Analysis (bioSkills) - Defines cytometry populations with manual or automated gates — hierarchical GatingSets, openCyto templates, flowDensity thresholds, and FlowJo round-tripping via CytoML
Gene Liability Evaluation (ToolUniverse Claude Skill) - ToolUniverse agent skill that scores the human safety liability of inhibiting or knocking out a gene across five evidence dimensions.
Gene Ontology MCP Server - Query GO terms, annotations, and enrichment inputs from the Gene Ontology; part of the Genes & Ontologies connector in Claude Science.
Generate Image (Claude Skill) - Generate or edit images using AI models (FLUX, Nano Banana 2).
GeoMaster (Claude Skill) - Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains.
GeoPandas (Claude Skill) - Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files.
Geometric Analysis (bioSkills) - Measure static protein structures with Bio.PDB — distances, dihedrals, superposition and RMSD, radius of gyration, and SASA — with the caveats stated
Get Available Resources (Claude Skill) - This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs …
Ginkgo Cloud Lab (Claude Skill) - Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs).
Glycoengineering (Claude Skill) - 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.
Guide to Pharmacology (GtoPdb) (Claude Skill) - Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs.
HCP Early-Psychosis Pipeline (Claude Skill) - End-to-end workflow for the HCP Early Psychosis (HCP-EP) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI
HCP Pipelines (Claude Skill) - Perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion) using the official HCP Pipelines
HCP Young-Adult Pipeline (Claude Skill) - End-to-end workflow for the HCP Young Adult (HCP-YA / HCP1200) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI
HCP-Aging Pipeline (Claude Skill) - End-to-end workflow for the HCP Aging (HCP-A) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI
HCP-Development Pipeline (Claude Skill) - End-to-end workflow for the HCP Development (HCP-D) dataset, including dataset download, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI
HMDB (Claude Skill) - Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping.
HOMER (Claude Skill) - De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER.
Harmony (Claude Skill) - Harmony batch correction for scRNA-seq and other omics.
Hashtag Demultiplexing (bioSkills) - Assign pooled single-cell data back to sample of origin from HTO, MULTI-seq or CellPlex tags and call cross-sample doublets
Healthy Brain Network (HBN) Pipeline (Claude Skill) - End-to-end workflow for the Healthy Brain Network (HBN) dataset, including download, BIDS organization, and multimodal processing of sMRI, dMRI, rs-fMRI, task-fMRI, and EEG data
Hierarchical Parcellation (Claude Skill) - Perform brain parcellation using Hierarchical clustering.
Hugging Science (Claude Skill) - The user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math …
Human Protein Atlas MCP Server - Query the Human Protein Atlas — tissue/blood/brain expression, subcellular localization, cancer markers, and antibody validation/staining data.
HypoGeniC (Claude Skill) - Automated LLM-driven hypothesis generation and testing on tabular datasets.
Hypothesis Crucible (Claude Plugin) - 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) - Structured hypothesis formulation from observations.
IBGNN (Claude Skill) - Run IBGNN (Interpretable Brain Graph Neural Network) for fMRI phenotype prediction.
ICA Decomposition (Claude Skill) - Perform resting-state network decomposition using ICA.
ICD-10 Codes MCP (Anthropic Healthcare) - Anthropic-published MCP server for ICD-10 diagnosis and procedure code lookup, sourced from CMS and CDC, for medical coding and claims workflows.
ISO 13485 Certification (Claude Skill) - Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems.
IXI Pipeline (Claude Skill) - End-to-end workflow for the IXI (Information eXtraction from Images) dataset, including data download, BIDS organization, and multimodal processing of T1w, T2w, and MRA
Imaging Data Commons (Claude Skill) - Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index.
Immcantation BCR Analysis (bioSkills) - 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) - 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) - 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.
Indication Dossier (Claude Skill) - Anthropic agent skill that compiles an indication/target dossier by orchestrating Claude Science connectors (Open Targets, ClinicalTrials, literature).
Inductive Bio ADMET Connector - Claude.ai connector surfacing Inductive Bio's ADMET prediction models so drug-discovery chemists can predict compound properties in-conversation.
Infographics (Claude Skill) - Create professional infographics using Nano Banana Pro AI with smart iterative refinement.
IntAct (Claude Science Connector) - Molecular-interaction evidence from EMBL-EBI's IntAct database; a source in the Structures & Interactions connector in Claude Science.
InterPro (Claude Skill) - Query InterPro REST API for protein domain architecture, family classification, and member-DB integration.
Interface Analysis (bioSkills) - Map protein-protein and protein-ligand interfaces with Bio.PDB — contact residues, buried surface area, and telling a real interface from crystal packing
JASPAR (Claude Skill) - JASPAR 2024 TF binding profiles via REST API and pyJASPAR.
K-means Parcellation (Claude Skill) - Perform brain parcellation using K-means.
KEGG Database (REST API) (Claude Skill) - KEGG REST API (academic only).
KEGG Pathway Analysis (Claude Skill) - Guide to KEGG pathway enrichment for DEG results.
Ketcher Chemistry (Claude Science Connector) - Interactive 2D molecule sketcher (Ketcher) for drawing/editing chemical structures; the Ketcher Chemistry connector in Claude Science.
Kraken2 Metagenomic Classification (bioSkills) - Classify shotgun metagenomic reads to taxa with Kraken2 minimizer/LCA matching, then re-estimate abundance with Bracken
LG-GNN (Claude Skill) - Run LG-GNN (Local-to-Global GNN) for fMRI phenotype prediction.
LIANA-MCP - MCP server wrapping LIANA so Claude can infer and plot cell-cell communication from single-cell data in natural language.
LaTeX Posters (Claude Skill) - Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter.
LabArchives (Claude Skill) - Electronic lab notebook API integration.
LaminDB (Claude Skill) - Working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.
LatchBio (Claude Skill) - Latch platform for bioinformatics workflows.
Lesion-Symptom Mapping Guide (Claude Skill) - Plan and run lesion-symptom mapping in patient cohorts — VLSM, multivariate SVR-LSM, disconnection and lesion network mapping
LigandMPNN (Claude Skill) - LigandMPNN ligand-aware protein sequence design (fixed-backbone) accounting for small molecules, metals, and nucleotides; a Claude Science skill.
Lineage Tracing (bioSkills) - Reconstruct single-cell lineage trees from CRISPR scars, expressed barcodes or mtDNA mutations using Cassiopeia, Startle and CoSpar
LiteParse (Claude Skill) - Local document and PDF parsing with spatial text and bounding boxes.
Literature Review (Claude Skill) - Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
MACS3 (Claude Skill) - Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs.
MATLAB / Octave (Claude Skill) - MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing.
MDAnalysis (Claude Skill) - Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS.
MDTraj (Claude Skill) - Mdtraj molecular dynamics trajectory analysis (Python).
MEG Processing (Claude Skill) - Process MEG (magnetoencephalography) data including source localization, time-frequency analysis, connectivity analysis, sensor-level preprocessing, or MEG-specific feature extraction
MGnify (Claude Science Connector) - 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) - 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) - 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
MNE-Python (EEG) (Claude Skill) - Execute concrete MNE-Python operations for EEG loading, preprocessing, filtering, artifact removal, epoching, frequency-band analysis, or feature extraction.
MOFA+ (Claude Skill) - Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2.
MS Lesion Segmentation Challenge Pipeline (Claude Skill) - End-to-end workflow for the Longitudinal MS Lesion Segmentation Challenge dataset, including data validation, multimodal processing of T1w, T2w, FLAIR, and PD, lesion segmentation, and …
MSA Statistics (bioSkills) - Compute percent identity, conservation scores, gap profiles and substitution-matrix statistics over a multiple alignment with BioPython, and read them correctly
MSI Detection (bioSkills) - Calls microsatellite instability from WES/WGS/panel or cfDNA with MSIsensor-pro, MANTIS and mSINGS for dMMR, Lynch screening and ICI eligibility
MarkItDown (Claude Skill) - Convert files and office documents to Markdown.
Markdown & Mermaid Writing (Claude Skill) - Comprehensive markdown and Mermaid diagram writing skill.
Materials Project MCP Server - MCP server for querying Materials Project crystal structures by formula, exporting CIF/POSCAR, and building supercells and moiré bilayers.
Matplotlib (Claude Skill) - Low-level plotting library for full customization.
MaxQuant (Claude Skill) - MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with …
MedChem (Claude Skill) - Claude skill wrapping MedChem — drug-likeness filters (Lipinski, Veber, Egan, Muegge), ADMET-flag detection, and medicinal-chemistry alerts on top of RDKit.
Medical Terminologies MCP - MIT-licensed MCP server giving Claude unified lookup and cross-mapping across ICD-11, SNOMED CT, LOINC, RxNorm, MeSH, and ATC.
Medicare MCP Server (OpenPharma) - MIT MCP server over public CMS Medicare data — provider and prescriber lookup, hospital quality and safety measures, Part B/D drug pricing and formularies.
Medidata Connector - Medidata's clinical-trial MCP connector — query platform documentation (Rave EDC, Data Connect) and predict high-enrollment trial sites during protocol planning.
Mendelian Randomization (ToolUniverse Claude Skill) - ToolUniverse agent skill that uses genetic variants as instrumental variables to test whether an exposure causally affects a disease outcome.
MetaPhlAn Profiling (bioSkills) - Profile shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4 clade-specific markers, with cell-fraction vs read-fraction and index-pinning guidance
MetaboLights (Claude Science Connector) - Metabolomics studies, metadata, and metabolite data from EMBL-EBI's MetaboLights; a source in the Omics Archives connector in Claude Science.
Metabolite Cell Communication (bioSkills) - Infer metabolite-mediated cell-cell crosstalk from scRNA-seq by scoring enzyme-to-sensor pairs with MEBOCOST, with explicit limits on what the result supports
Metabolomics Workbench (Claude Skill) - Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.
MiXCR Analysis (bioSkills) - 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
Missing Data Sensitivity (bioSkills) - Run regulatory-grade missing-data analyses for confirmatory trials — MMRM, reference-based multiple imputation, tipping-point and pattern-mixture sensitivity
Modal (Claude Skill) - Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs.
Molecular Dynamics (Claude Skill) - Claude skill that runs and analyzes OpenMM molecular dynamics simulations and MDAnalysis trajectory analyses for proteins, ligands, and biomolecular complexes.
Molecule-MCP - MCP bundle letting Claude drive PyMOL and ChimeraX visualization and run GROMACS molecular dynamics simulations via natural language.
Molfeat (Claude Skill) - Claude skill wrapping Molfeat — a unified API over 100+ molecular featurizers spanning classical fingerprints, descriptors, and pre-trained chemical foundation-model embeddings.
Momentum FHIR MCP Server - MIT-licensed FHIR R4 MCP server with full CRUD, document ingestion/chunking, and Pinecone-backed semantic search over clinical records.
Monarch Initiative (Claude Skill) - Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.
Morning (Claude Skill) - Anthropic 'morning brief' agent skill that assembles a daily briefing from the user's own calendar and mail connectors; used in Claude Science.
Motor Neuron Disease (MND) Pipeline (Claude Skill) - End-to-end workflow for the Motor Neuron Disease (MND) dataset from OpenNeuro ds005874, including BIDS validation, multimodal processing of rs-fMRI and task-fMRI, phenotype extraction, and …
Mouse Phenome Database (Claude Skill) - Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.
MultiQC (Claude Skill) - Aggregates QC from 150+ bioinformatics tools into one interactive HTML report.
Multiple Sequence Alignment (bioSkills) - Build multiple sequence alignments with MAFFT, MUSCLE5, Clustal Omega or T-Coffee, choosing the algorithm by dataset size and divergence
Multiplicity and Graphical Procedures (bioSkills) - Build the multiplicity strategy for confirmatory trials — graphical Bretz-Maurer-Hommel procedures, gatekeeping and Holm/Hochberg/Hommel — with gMCP and FDA 2022 guidance
MyGene.info MCP (BioThings) - Gene annotation and ID conversion across species via MyGene.info/BioThings; the Genes & Ontologies connector in Claude Science.
NCBI GEO - NCBI GEO access — keyword/series search, GSE matrices, GPL/GSM metadata — as a SciAgent skill or the MCPmed GEO MCP server.
NCBI Gene (Claude Skill) - NCBI Gene via E-utilities: curated records across 1M+ taxa.
NIFD (Frontotemporal Dementia) Pipeline (Claude Skill) - End-to-end workflow for the Neuroimaging in Frontotemporal Dementia (NIFD) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration
NPI Registry MCP (Anthropic Healthcare) - Anthropic-published MCP server over the CMS NPPES NPI Registry — validate, look up, and search US healthcare providers by National Provider Identifier.
NWB MCP Server - Query local, S3, or DANDI-hosted NWB neurophysiology files as a virtual SQL database, read-only, without writing Python.
Natural Scenes Dataset (NSD) Pipeline (Claude Skill) - End-to-end workflow for the Natural Scenes Dataset (NSD), including data access, BIDS validation, multimodal processing of task-fMRI and structural MRI, stimulus metadata extraction, and …
Neoantigen Prediction (bioSkills) - Identify tumor neoantigens from somatic variants with pVACtools for personalized cancer vaccines and checkpoint biomarkers, centering clonality, HLA LOH, expression, and validation tiers
NetNeuroTools Guide (Claude Skill) - Network neuroscience with netneurotools — consensus connectomes, graph metrics, modularity, spatial autocorrelation-preserving null models and permutation statistics
NetworkX (Claude Skill) - Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python.
Neural Population Analysis Guide (Claude Skill) - Choose and validate dimensionality-reduction methods for neural population recordings — PCA, GPFA, dPCA and jPCA — with principled dimensionality selection
NeuroFlow - End-to-end Claude Code plugin for neuroscience research — ideation, grant writing, experiment design, data analysis, computational brain modeling, and paper drafting.
NeuroHarmonize (ComBat) (Claude Skill) - Remove site/scanner/batch effects from neuroimaging features before running downstream models, run mega-analysis across multiple datasets, or evaluate models with leave-site-out / site-stratified protocols
NeuroKit2 (Claude Skill) - Claude skill for biosignal processing — ECG, EEG, EDA, RSP, PPG, EMG, and EOG analysis including HRV, event-related responses, and multi-modal physiological insights.
NeuroSTORM (Claude Skill) - Run the NeuroSTORM multi-model fMRI platform: preprocessing, pretraining (MAE or contrastive), fine-tuning, inference, or benchmarking.
Neuropixels-Analysis (Claude Skill) - Claude skill for end-to-end Neuropixels analysis — SpikeGLX/Open Ephys/NWB loading, preprocessing, motion correction, and Kilosort4/SpykingCircus2/Mountainsort5 spike sorting.
Neurosift Tools MCP - MCP server that lets Claude search DANDI/OpenNeuro and introspect NWB neurophysiology files, plus semantic search over PyNWB docs.
NiBabel (Claude Skill) - NeuroClaw needs concrete nibabel operations for neuroimaging files: loading and validating NIfTI images, inspecting shapes and affine matrices, saving derived images, converting voxel coordinates …
Nilearn (Claude Skill) - Execute concrete Nilearn operations: ROI/atlas time-series extraction, confounds handling (fMRIPrep), seed-based connectivity maps, ROI-to-ROI connectivity matrices, and optional GLM/decoding utilities.
NovoMCP - Hosted computational-chemistry engine MCP — ADMET, GFN2-xTB QM, GPU GROMACS MD, and AutoDock-GPU docking over a precomputed compound layer.
OASIS Pipeline (Claude Skill) - End-to-end workflow for the OASIS (Open Access Series of Imaging Studies) dataset, including BIDS validation, multimodal processing of sMRI, and phenotype extraction for aging …
OMERO (Claude Skill) - Microscopy data management platform.
OMOPHub MCP Server - Search, map and navigate 10M+ OHDSI OMOP vocabulary concepts (SNOMED CT, ICD-10, RxNorm, LOINC) from Claude without loading ATHENA locally
Omics Analysis Guide (Claude Skill) - Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
Ontology Lookup Service (OLS) MCP Server - Search and resolve terms across hundreds of biomedical ontologies via EMBL-EBI's OLS; part of the Genes & Ontologies connector in Claude Science.
Open Notebook (Claude Skill) - Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis.
Open Targets (Claude Skill) - Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety.
Open Targets Plugin - Official Open Targets MCP plugin giving Claude GraphQL access to target-disease associations, drug evidence, and target-prioritisation scores.
OpenAlex (Claude Skill) - Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts.
OpenCV (Bio-image) (Claude Skill) - Computer vision for bio-image preprocessing, feature detection, real-time microscopy.
OpenFDA MCP Server (cyanheads) - Apache-2.0 MCP server federating the full openFDA API — drugs, food, devices (510k/PMA), veterinary, recalls, and shortages — with a public HTTP instance.
OpenFDA MCP Server (ythalorossy) - MIT-licensed npm MCP server over the openFDA drug API — adverse events, safety/labeling, manufacturer lookups, and NDC resolution.
OpenFold3 (Claude Skill) - OpenFold3 open-source biomolecular structure prediction (AlphaFold-class), run locally; a Claude Science skill.
OpenMM MCP Server - MCP server that sets up and runs OpenMM molecular dynamics simulations (protein, membrane, advanced sampling) and Abacus DFT jobs from natural language.
OpenNeuro MCP - Community MCP server giving Claude GraphQL access to the OpenNeuro archive of MRI, MEG, EEG, iEEG, and ECoG datasets.
Opentrons (Claude Skill) - Official Opentrons Protocol API for OT-2 and Flex robots.
Optimize for GPU (Claude Skill) - GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT.
Optogenetics Protocol Designer (Claude Skill) - Choose opsins, wavelengths, pulse protocols, fiber specifications and control conditions for optogenetic excitation or inhibition experiments
Owkin Pathology Explorer Connector - Owkin's Pathology Explorer agent — H&E whole-slide image analysis, cell-type detection, and tumour-microenvironment profiling — exposed to Claude as a remote MCP connector.
PBMCpedia MCP - Query PBMCpedia's harmonized PBMC single-cell atlas — per-cell-type expression, DEGs, pathways and antibody chains — filtered by sex, age and disease.
PDB MCP Server - MCP servers that let Claude search, fetch, and validate RCSB Protein Data Bank structures — including the official first-party RCSB server.
PDBe MCP Servers - First-party PDBe Europe MCP servers giving Claude access to protein structure data via REST API, Solr search, and an optional Neo4j graph.
PDF (Claude Skill) - The user wants to do anything with PDF files.
PET Processing (Claude Skill) - Process PET neuroimaging data including spatial normalization to T1w/MNI space, SUVR computation, reference region quantification, partial volume correction, or tracer-specific workflows (PiB amyloid, FDG …
PLINK2 (Claude Skill) - GWAS and population genetics tool.
PNC Pipeline (Claude Skill) - End-to-end workflow for the Philadelphia Neurodevelopmental Cohort (PNC) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, task-fMRI, and dMRI, phenotype extraction, and QC integration
PPMI Pipeline (Claude Skill) - End-to-end workflow for the Parkinson's Progression Markers Initiative (PPMI) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration
PPTX (Claude Skill) - A .pptx file is involved in any way — as input, output, or both.
PPTX Posters (Claude Skill) - Create research posters using HTML/CSS that can be exported to PDF or PPTX.
PRIDE (Claude Skill) - Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata …
Paper Lookup (Claude Skill) - Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.
Parallel Web (Claude Skill) - All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources.
Parameter Recovery Checker (Claude Skill) - Run parameter- and model-recovery simulations to check a cognitive model is identifiable before you interpret its fitted parameters
PathML (Claude Skill) - Full-featured computational pathology toolkit.
Pathway Enrichment (Claude Skill) - Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results.
Peer Review (Claude Skill) - Structured manuscript/grant review with checklist-based evaluation.
PennyLane (Claude Skill) - Hardware-agnostic quantum ML framework with automatic differentiation.
Perturb-seq Analysis (bioSkills) - Analyze single-cell CRISPR screens with Pertpy, Mixscape escaper removal, SCEPTRE calibrated testing and E-distance effect sizes
Pharmacovigilance (ToolUniverse Claude Skill) - ToolUniverse agent skill that mines FAERS adverse-event reports and FDA labels, computes disproportionality signals (PRR, ROR, IC), and assesses pharmacogenomic risk.
Phylogenetics (Claude Skill) - Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML).
Plotly (Claude Skill) - Interactive scientific visualization with Plotly.
Polars (Claude Skill) - Fast in-memory DataFrame library for datasets that fit in RAM.
Polars-Bio (Claude Skill) - High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames.
Power and Sample Size (bioSkills) - Size superiority, non-inferiority and equivalence trials for continuous, binary and survival endpoints, with FDA M1/M2 margin logic and CONSORT-ready justification
Precision Oncology (ToolUniverse Claude Skill) - ToolUniverse agent skill that maps a tumor molecular profile to matched FDA-approved/investigational therapies, resistance mechanisms, and clinical trials.
PrimeKG (Claude Skill) - Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
Procedure Coding (Anthropic Healthcare Plugin) - Anthropic Claude skill that converts a clinical encounter's documentation into claim-ready CPT and HCPCS Level II procedure codes the way a professional coder would.
Prokka (Claude Skill) - Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline.
Protein MCP Server - Federated protein-structure search across experimental (PDB) and predicted (AlphaFold) models — homolog search, structural alignment, ligand and annotation lookup, keyless.
ProteinMPNN (Claude Skill) - ProteinMPNN deep-learning fixed-backbone protein sequence design; runs locally as a Claude Science skill.
Protocols.io (Claude Skill) - Integration with protocols.io API for managing scientific protocols.
PubChem MCP Server - MCP server that lets Claude query PubChem for compounds by name, SMILES, CID, or formula and pull structure files.
PufferLib (Claude Skill) - High-performance reinforcement learning framework optimized for speed and scale.
PyDESeq2 (Claude Skill) - Claude skill for bulk RNA-seq differential expression with PyDESeq2 — size factors, dispersion, Wald / LRT testing, BH-adjusted p-values.
PyHealth (Claude Skill) - Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep …
PyImageJ / Fiji (Claude Skill) - Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops.
PyLabRobot (Claude Skill) - Vendor-agnostic lab automation framework.
PyMC (Claude Skill) - Bayesian modeling with PyMC.
PyMOL (Claude Skill) - Visualize, align, and render protein/molecular structures with PyMOL — headless, GPU-free, producing publication-quality PNGs and editable .pse sessions.
PyTDC (Claude Skill) - Claude skill driving PyTDC for Therapeutics Data Commons benchmarks — ADMET, drug-target / drug-drug interactions, drug response, molecular generation, retrosynthesis.
PyTorch Geometric (Claude Skill) - PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets.
PyTorch Lightning (Claude Skill) - Deep learning framework (PyTorch Lightning / lightning package).
Pycortex Guide (Claude Skill) - Render fMRI data on cortical surfaces with pycortex — 2D flatmaps, interactive 3D WebGL viewers, volume-to-surface mapping and ROI management
Pymatgen (Claude Skill) - Materials science toolkit.
QSIPrep (Claude Skill) - Run QSIPrep (BIDS App) for diffusion MRI (DWI) preprocessing with best-practice workflows (topup/eddy, denoising/unringing options, susceptibility/motion correction, coregistration/normalization, QC reports) on BIDS datasets.
Qiskit (Claude Skill) - IBM quantum computing framework.
QuTiP (Claude Skill) - Quantum physics simulation library for open quantum systems.
QuickGO (Claude Skill) - Query EBI QuickGO REST API for GO terms and protein annotations.
RDKit Agent - WASM-based cheminformatics CLI, Node library, and MCP server that validates, converts, and analyzes SMILES/SMIRKS/InChI with no Python runtime.
RDKit Cheminformatics Skill - Claude skill providing RDKit recipes for SMILES parsing, descriptors, fingerprints, substructure search, reactions, and 2D/3D molecular generation.
RDKit MCP Server - MCP server exposing the full RDKit API as discrete tool calls so Claude can run cheminformatics without executing Python locally.
REST-meta-MDD Pipeline (Claude Skill) - End-to-end workflow for the REST-meta-MDD (Resting-State Meta-Major Depressive Disorder) dataset, including BIDS validation, processing of rs-fMRI, phenotype extraction, and QC integration
RNA Structure Probing (bioSkills) - Turn SHAPE-MaP or DMS-MaPseq reads into per-nucleotide reactivity profiles with ShapeMapper2, then fold RNA with those reactivities as soft restraints
Rare Disease Diagnosis (ToolUniverse Claude Skill) - ToolUniverse agent skill for rare-disease differential diagnosis — HPO phenotype matching to Orphanet/OMIM, gene-panel prioritization, and ACMG variant interpretation.
Rare Disease Genomics (ToolUniverse Claude Skill) - ToolUniverse agent skill for rare-disease investigation — Orphanet characterization, HPO phenotypes, causative genes, GenCC validity, ClinVar variants, trials, and repurposing.
ReMap (Claude Skill) - Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.
Reactome (Claude Skill) - Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs.
RegulomeDB (Claude Skill) - Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs …
Repertoire Visualization (bioSkills) - Render TCR/BCR repertoire figures — V-J chord diagrams, spectratypes, clonal tracking, rarefaction curves, overlap heatmaps and similarity networks — with depth-robust metric guidance
Research Grants (Claude Skill) - Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC.
Research Lookup (Claude Skill) - Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-search (academic paper searches).
Revvity Signals AI Connector - Claude.ai connector giving natural-language access to the Revvity Signals electronic lab notebook and connected R&D data.
Rfam (Claude Science Connector) - Non-coding RNA families, covariance models, and alignments from EMBL-EBI's Rfam; the RNA connector in Claude Science.
Rhea (Claude Science Connector) - Expert-curated biochemical reactions from Rhea (SIB); a source in the Chemistry connector in Claude Science.
Roary (Claude Skill) - Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline.
Rosetta MCP Server - MCP server for Rosetta, PyRosetta and Biotite — run and validate RosettaScripts, score structures, translate protocols between the three APIs
Rowan - Cloud-native molecular modeling and medicinal-chemistry workflow platform, installable as a Claude Skill or an MCP server.
Run Models (NeuroClaw) (Claude Skill) - Run phenotype-prediction models, browse model cards, map model inputs/outputs, or choose an execution route for fMRI/sMRI based models.
SAMtools (Claude Skill) - CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.
SAR Analysis (Claude Skill) - Structure-activity relationship (SAR) analysis guide for drug discovery including molecular descriptor analysis, scaffold analysis, and activity cliff detection
SEED-IV (EEG Emotion) Pipeline (Claude Skill) - End-to-end workflow for the SEED-IV (SJTU Emotion EEG Dataset - 4 emotions) dataset, including EEG validation, preprocessing, feature extraction, and emotion classification
SEED-VIG (EEG Vigilance) Pipeline (Claude Skill) - End-to-end workflow for the SEED-VIG (SJTU Emotion EEG Dataset - Vigilance) dataset, including EEG validation, preprocessing, feature extraction, and vigilance/fatigue detection
SHAP (Claude Skill) - Model interpretability and explainability using SHAP (SHapley Additive exPlanations).
STAR (Claude Skill) - Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables.
STRING (Claude Skill) - Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species).
SVM Classifier (Claude Skill) - Perform disease classification with SVM.
Salmon (Claude Skill) - Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM).
Scanpy-MCP - MCP server wrapping Scanpy so Claude can run end-to-end single-cell RNA-seq analyses (QC, clustering, DE, plotting) from natural language.
Scholar Evaluation (Claude Skill) - Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative …
Scholar Gateway Connector (Wiley) - Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.
SciTeX Dataset MCP - MCP server giving Claude a unified search across OpenNeuro, DANDI, PhysioNet, and Zenodo for BIDS/NWB neuroscience datasets.
Scientific Brainstorming (Claude Skill) - Creative research ideation and exploration.
Scientific Critical Thinking (Claude Skill) - Evaluate scientific claims and evidence quality.
Scientific Schematics (Claude Skill) - Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement.
Scientific Slides (Claude Skill) - Build slide decks and presentations for research talks.
Scientific Visualization (Claude Skill) - Meta-skill for publication-ready figures.
Scientific Writing (Claude Skill) - Core skill for the deep research and writing tool.
Seaborn (Claude Skill) - Statistical visualization with pandas integration.
Seqera MCP - Hosted MCP server for launching and managing Nextflow/nf-core pipelines on the Seqera Platform and retrieving public SRA/ENA/GEO sequencing data.
Signal Detection Analysis (Claude Skill) - Apply signal detection theory to behavioral data — d-prime, criterion, beta, extreme-value correction and non-parametric alternatives
Signal Detrending (Claude Skill) - Perform neuroimaging signal denoising with classical detrending methods.
SimPy (Claude Skill) - Process-based discrete-event simulation framework in Python.
SimpleITK (Claude Skill) - Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal.
Single-Cell Annotation Guide (Claude Skill) - Decision framework for manual marker-based, automated (CellTypist), and reference-based (popV) cell type annotation in scRNA-seq.
Small Molecule Discovery (ToolUniverse Claude Skill) - ToolUniverse agent skill for compound identification, analog search, bioactivity, ADMET, target prediction, and commercial sourcing across PubChem, ChEMBL, BindingDB, and vendor catalogs.
Snakemake (Claude Skill) - Python-based workflow manager for reproducible, scalable pipelines.
SnpEff / SnpSift (Claude Skill) - Annotate and filter VCF variants with SnpEff and SnpSift.
SolubleMPNN (Claude Skill) - Soluble-optimized ProteinMPNN weights that bias sequence design away from exposed hydrophobics; a Claude Science skill.
Somatic Signatures (bioSkills) - Extracts and assigns COSMIC v3.4 mutational signatures from somatic VCFs with SigProfiler, MutationalPatterns, MuSiCal or HRDetect to read DNA-damage etiology
SpaceNet Classifier (Claude Skill) - Perform disease classification with SpaceNet.
Specificity Annotation (bioSkills) - Annotate TCR/BCR sequences against antigen-specificity databases and cluster by shared-specificity signal, treating matches as hypotheses with generation-probability nulls
SpikeInterface (Claude Skill) - Unified Python framework for extracellular electrophysiology.
SpikeLab - Agent-skill suite for multi-electrode-array spike-train analysis and spike sorting (Kilosort2/4, RT-Sort), with an optional built-in MCP server.
Stable-Baselines3 (Claude Skill) - Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API.
Statistical Analysis (Claude Skill) - Guided statistical analysis with test selection and reporting.
Strain Tracking (bioSkills) - Resolve and compare bacterial strains below species level from shotgun metagenomes using inStrain popANI, StrainPhlAn, MIDAS2, StrainGE and skani/fastANI
Structural Alignment (bioSkills) - Superpose and score protein structures with Foldseek, TM-align, US-align, DALI or FoldMason when sequence identity is too low to align reliably
Structural MRI (sMRI) (Claude Skill) - Process structural MRI (sMRI) such as T1w/T2w/FLAIR for brain extraction, bias correction, tissue segmentation (GM/WM/CSF), registration to MNI, cortical/subcortical parcellation, cortical thickness/volumetry (FreeSurfer), HCP-style …
Structure Preparation (bioSkills) - Make a deposited or predicted structure docking- or MD-ready with PDBFixer, reduce, PROPKA and PDB2PQR — hydrogens, tautomers, missing atoms, short loops
Structure Validation (bioSkills) - Decide whether a structure or region is reliable enough to build on — resolution, R-free gap, B-factors, MolProbity geometry, and pLDDT/PAE for predicted models
Subgroup Analysis (bioSkills) - Run subgroup and heterogeneous-treatment-effect analyses — interaction tests, RERI, causal forests, Bayesian shrinkage — against the Sun BMJ and EMA 2019 credibility criteria
SymPy (Claude Skill) - You need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX.
Synapse.org Connector - Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.
TAD Detection (bioSkills) - Call TAD boundaries from balanced Hi-C matrices with cooltools insulation scores, including the window sweep and boundary-strength ranking
TCR-Epitope Binding (bioSkills) - 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
Target Research (ToolUniverse Claude Skill) - ToolUniverse agent skill that profiles a drug target across nine parallel research paths — expression, pathways, interactions, variants, druggability — into a cited report.
Taxonomy Assignment (bioSkills) - 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
Temporal Filtering (Claude Skill) - Perform neuroimaging signal denoising with classical temporal filtering methods.
TileDB-VCF (Claude Skill) - Efficient storage and retrieval of genomic variant data using TileDB.
TimesFM (Claude Skill) - Zero-shot time series forecasting with Google's TimesFM foundation model.
ToolUniverse - Harvard / MIT MCP server bundling 600+ vetted scientific tools — literature, chemistry, omics, clinical trials — for AI-scientist-style hypothesis exploration.
TorchDrug (Claude Skill) - PyTorch-native graph neural networks for molecules and proteins.
Transdiagnostic Connectome Project (TCP) Pipeline (Claude Skill) - End-to-end workflow for the Transdiagnostic Connectome Project (TCP) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, and dMRI, phenotype extraction, and QC integration
Transformers (Hugging Face) (Claude Skill) - Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks.
Treatment Plans (Claude Skill) - Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties.
Trial Reporting (bioSkills) - Produce CONSORT 2025 / ICH E9(R1)-conformant trial statistical reports: estimands, analysis populations, Table 1, MMRM, and multiplicity control
Tumor Mutational Burden (bioSkills) - Calculates TMB from WES/WGS/panel data with Friends of Cancer Research harmonization, per-assay calibration, hypermutator tiering and blood TMB
UCLA CNP Pipeline (Claude Skill) - End-to-end workflow for the UCLA CNP (Consortium for Neuropsychiatric Phenomics) dataset, including BIDS validation, multimodal processing of sMRI, task-fMRI, and dMRI, phenotype extraction, and …
UCSC Cell Browser MCP - Search the UCSC Cell Browser's public single-cell dataset collection by organism, tissue, disease or project, and pull per-dataset metadata.
UCSC Genome Browser (Claude Skill) - Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.
UK Biobank (Brain) Pipeline (Claude Skill) - Analyze already available UK Biobank data for brain-related research, including neurological outcomes, cognitive phenotypes, brain MRI derived phenotypes, survival analysis, subgroup analysis, propensity score …
UMAP-learn (Claude Skill) - UMAP dimensionality reduction.
US Fiscal Data (Claude Skill) - Query the U.S.
USPTO Patents (Claude Skill) - Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery).
UniChem (Claude Skill) - Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API.
UniProt MCP Server - 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) - Compute depth-normalized TCR/BCR repertoire diversity (Hill profiles), overlap, clonality and segment usage with VDJtools/immunarch, with estimator and normalization guidance
Vaex (Claude Skill) - Processing and analyzing large tabular datasets (billions of rows) that exceed available RAM.
Venue Templates (Claude Skill) - Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR …
ViennaRNA (Claude Skill) - Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.
WMH Segmentation (Claude Skill) - Perform automated white matter hyperintensity (WMH) segmentation on structural MRI data using the MARS-WMH nnU-Net model.
WSO2 FHIR MCP Server - Open-source MCP bridge that lets Claude search, read, and write FHIR R4 resources against any EHR or sandbox FHIR API with SMART-on-FHIR auth.
Western Blot Quantification (Claude Skill) - Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods
What-If Oracle (Claude Skill) - Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order).
XLSX (Claude Skill) - Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) where the workbook file is the primary deliverable.
XTB MCP Server - MCP server that builds, validates, and explains xtb semi-empirical quantum-chemistry input decks for optimizations, frequencies, MD, and spectroscopy.
ZINC (Claude Skill) - Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable).
Zarr-Python (Claude Skill) - Chunked N-D arrays for cloud storage (Zarr-Python 3).
aeon (Claude Skill) - Time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search.
allenbrain-mcp - Community MCP wrapper exposing Allen Brain Atlas RMA queries, cell-types, mouse connectivity, ontologies, and image/grid downloads to Claude.
arXiv MCP Server - Search and retrieve arXiv preprints (incl. q-bio) and metadata; part of the Literature Graph connector in Claude Science.
bio-research (Claude Code Plugin) - Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.
bioRxiv / medRxiv (Claude Skill) - Query bioRxiv/medRxiv preprints via REST API.
cBioPortal (Claude Skill) - Cancer genomics (TCGA et al.) via cBioPortal REST API.
cBioPortal MCP Server - Query cancer genomics studies, mutations, and clinical data from cBioPortal; also the Cancer Models connector in Claude Science.
clinical-trial-protocol (Anthropic Healthcare Plugin) - Anthropic Claude Code plugin that drafts FDA/NIH-compliant Phase 2/3 clinical-trial protocols for drugs or devices via a waypoint-based workflow.
dbSNP (Claude Skill) - Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.
dcm2niix (DICOM → NIfTI) (Claude Skill) - Convert DICOM files or folders to NIfTI format (.nii or .nii.gz), extract neuroimaging volumes from clinical DICOM series (MRI, CT, PET, etc.), prepare raw …
decoupler-MCP - MCP server wrapping decoupler so Claude can infer pathway and transcription-factor activities from expression data in natural language.
deepTools (Claude Skill) - NGS analysis toolkit.
eQTL Catalogue (Claude Science Connector) - Uniformly processed cis-QTL (eQTL/sQTL) summary statistics from EMBL-EBI's eQTL Catalogue; a source in the Human Genetics connector in Claude Science.
fMRI Processing (Claude Skill) - Perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox
fMRIPrep (Claude Skill) - Perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep
fastp (Claude Skill) - All-in-one FASTQ QC and adapter trimming.
featureCounts (Claude Skill) - Counts RNA-seq reads overlapping GTF gene features.
fhir-developer (Anthropic Healthcare Plugin) - Anthropic Claude Code plugin for authoring FHIR R4 resources with LOINC, SNOMED, and RxNorm validation.
geniml (Claude Skill) - Working with genomic interval data (BED files) for machine learning tasks.
gget (Claude Skill) - Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.
gnomAD (Claude Skill) - GnomAD v4 population variant frequencies via GraphQL API.
gtars (Claude Skill) - High-performance toolkit for genomic interval analysis in Rust with Python bindings.
histolab (Claude Skill) - Lightweight WSI tile extraction and preprocessing.
instrument-data-to-allotrope - Converts 40+ lab-instrument output formats to Allotrope Simple Model JSON / CSV for LIMS and data-lake ingestion.
libSBML (Claude Skill) - Build, read, validate, modify SBML biological network models via the libSBML Python API.
matchms (Claude Skill) - Spectral similarity and compound identification for metabolomics.
mcptools (R) - Posit's CRAN package that turns a live R session into an MCP server, letting Claude run R and call your own R functions as tools.
muon (Claude Skill) - Multi-modal single-cell analysis with muon/MuData.
napari (Claude Skill) - Interactive viewer for microscopy.
ncRNA Search (bioSkills) - Find non-coding RNA homologs and assign Rfam families with Infernal covariance models, scoring sequence and secondary structure together
neuro-mcp - 54-tool MCP server wrapping MNE-Python EEG/MEG preprocessing, source imaging, a BIDS/EHR record store, and offline interactive plots.
nextflow-development - Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.
nii2dcm (NIfTI → DICOM) (Claude Skill) - Convert NIfTI files (.nii or .nii.gz) to DICOM format, create DICOM series from processed neuroimaging results, write segmentation/registration/analysis outputs back to DICOM for PACS …
nnU-Net (Claude Skill) - Medical image segmentation with nnU-Net's self-configuring framework — auto-selects architecture, preprocessing, training for any modality.
openFDA (Claude Skill) - Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement.
pLannotate (Claude Skill) - Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene).
pacsomatic (Claude Skill) - Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.
popV (Claude Skill) - Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting.
prior-auth-review (Anthropic Healthcare Plugin) - Anthropic Claude Code skill (in the consolidated healthcare plugin) that reviews prior-authorization request documents and surfaces gaps against payer rules.
pyNIBS (Claude Skill) - Analyze non-invasive brain stimulation (TMS/NIBS) experiments in pyNIBS — mesh/ROI I/O, coil-placement optimization, and MEP-to-E-field regression mapping.
pyOpenMS (Claude Skill) - Complete mass spectrometry analysis platform.
pydicom (Claude Skill) - Python library for working with DICOM (Digital Imaging and Communications in Medicine) files.
pymoo (Claude Skill) - Multi-objective optimization framework.
pyomop - Python OMOP CDM toolkit that ships an MCP server, letting Claude inspect and run SQL against an OHDSI CDM database on SQLite, PostgreSQL or MySQL
pysam (Claude Skill) - Genomic file toolkit.
pyzotero (Claude Skill) - Interact with Zotero reference management libraries using the pyzotero Python client.
scATAC Analysis (bioSkills) - Process single-cell ATAC-seq with Signac, ArchR or SnapATAC2 — fragment QC, TF-IDF/LSI, consensus peaks and chromVAR motif deviations
scGPT (Claude Skill) - scGPT single-cell foundation model for cell-type annotation, integration, and perturbation prediction; runs locally as a Claude Science skill.
scVelo (Claude Skill) - Claude skill for RNA-velocity analysis with scVelo — estimates cell-state transitions from unspliced/spliced mRNA counts, infers trajectories, latent time, and driver genes.
scientific-problem-selection - Structured framework for research project ideation, risk assessment, and troubleshooting, based on Fischbach & Walsh (Cell 2024).
scikit-bio (Claude Skill) - Skill for microbiome ecology — reads BIOM/FASTA, computes alpha/beta diversity (UniFrac), PCoA, PERMANOVA, and builds phylogenetic trees.
scikit-image (Claude Skill) - Python image processing for microscopy and bioimage analysis.
scikit-learn (Claude Skill) - Machine learning in Python with scikit-learn.
scikit-survival (Claude Skill) - Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival.
scirpy Analysis (bioSkills) - 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 - Deep-learning workflows for scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, and related scvi-tools models for single-cell omics.
sgRNA Design (Claude Skill) - Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments
single-cell-rna-qc - scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.
smina (Claude Skill) - Smina molecular docking CLI.
statsmodels (Claude Skill) - Statistical models library for Python.
trackpy (Claude Skill) - Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm.

All tools

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