Molecular and Cellular Biology
Installable Claude components for genomics, transcriptomics, single-cell analysis, gene regulation, CRISPR design, cell imaging, and other molecular- and cell-scale biology applications.
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.
A/B Compartment Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
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
ARCHS4 (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples.
Aging and Senescence Research (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA
ToolUniverse agent skill for geroscience — senescence markers, aging hallmarks, longevity GWAS, and senolytic target discovery with graded evidence.
Alignment Trimming (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
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 · 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.
AlphaFold2 (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: works · security: cleared
AlphaFold2 protein/complex structure prediction, run locally or via a hosted API with an optional ColabFold MSA server; a Claude Science skill.
AlphaGenome Single-Variant Analysis (Claude Skill)
Claude Skill · Google DeepMind · Preview · verified: degraded · security: cleared
Predict non-coding variant effects on expression, chromatin accessibility, histone marks, splicing, and TF binding via the AlphaGenome API.
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.
Arboreto (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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
MCP server · Augmented Nature · Beta · verified: works · security: caution
Search functional-genomics studies and metadata in ArrayExpress/BioStudies; part of the Omics Archives connector in Claude Science.
BCFtools (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: caution
CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats.
BEDTools (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Genomic interval ops on BED/BAM/GFF/VCF.
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.
BRENDA (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data.
BWA-MEM2 (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Fast short-read DNA aligner for WGS/WES/ChIP-seq.
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.
Benchling (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.
BioBank Japan (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
East Asian biobank GWAS summary statistics from BioBank Japan (PheWeb); a source in the Human Genetics connector in Claude Science.
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.
BioMart (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Bulk biological data-mining and ID mapping via Ensembl BioMart; the BioMart connector in Claude Science.
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.
Borzoi (Claude Skill)
Claude Skill · Calico Life Sciences · GA · verified: works · security: cleared
Borzoi sequence-to-expression model predicting RNA-seq coverage from DNA sequence; runs locally as a Claude Science skill.
Bulk RNA-seq (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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 …
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.
CIViC (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Crowd-curated clinical interpretations of cancer variants from CIViC (WashU); a source in the Clinical Genomics connector in Claude Science.
CNV Inference (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
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)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).
COBRApy (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Claude skill driving COBRApy for constraint-based metabolic modelling — FBA, FVA, gene knockouts, flux sampling, gapfilling on SBML genome-scale models.
COSMIC (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: caution
Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.
Cancer Genomics TCGA (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
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)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
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)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that ranks cancer cell lines for an experiment by cross-referencing DepMap, Cellosaurus, COSMIC, and PharmacoDB.
CellChat (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Infer and visualize intercellular communication from scRNA-seq with CellChat (R).
CellRank-MCP
MCP server · scmcphub · GA · verified: works · security: caution
MCP server wrapping CellRank so Claude can model cell fate and trajectories from single-cell data in natural language.
CellTypist (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Automated scRNA-seq cell type annotation via pre-trained logistic regression.
Cellpose (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
DL cell/nucleus segmentation for fluorescence and brightfield microscopy.
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.
ChatSpatial
MCP server · Chen Yang (cafferychen777) · GA · verified: works · security: cleared
MCP server for spatial transcriptomics — preprocessing, spatial domains, deconvolution, cell-cell communication, and SVG detection via Scanpy/Squidpy.
Chromatin Loop Calling (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Call focal chromatin loops from Hi-C or Micro-C maps with cooltools dots, chromosight and Mustache, and validate them with aggregate peak analysis
Clair Variant Caller (Claude Skill)
Claude Skill · HKU-BAL · GA · verified: works · security: caution
Agent skill for the Clair suite — germline, somatic, mosaic, and long-read RNA variant calling with Clair3/ClairS/Clair-Mosaic.
ClinGen (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Expert-curated gene–disease validity and variant clinical significance from ClinGen; a source in the Clinical Genomics connector in Claude Science.
ClinVar (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations.
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
Complex Portal (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Curated macromolecular complexes from EMBL-EBI’s Complex Portal; a source in the Structures & Interactions connector in Claude Science.
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.
Covariation Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
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)
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
DESeq2 (R/Bioconductor) (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Bulk RNA-seq DE with R/Bioconductor DESeq2.
DNAnexus (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
DNAnexus cloud genomics platform.
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.
DepMap (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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.
Dose-Response Analysis (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
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)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Flag and remove droplets containing two or more cells in single-cell RNA-seq using scDblFinder, Scrublet and DoubletFinder before clustering
Drug Mechanism Research (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that traces a drug’s mechanism from primary target through off-targets, pathways, FDA label, and pharmacogenomics.
Drug Target Validation (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that scores a drug target 0–100 across genetic, druggability, safety, and clinical-precedent gates with a GO/NO-GO recommendation.
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.
ENA (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
ENA REST API for sequences, reads, assemblies, and annotations.
ENCODE (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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
Claude Code Plugin · ammawla · Beta · verified: works · security: caution
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.
ESMFold (Claude Skill)
Claude Skill · Meta AI / EvolutionaryScale · GA · verified: works · security: caution
ESMFold single-sequence protein structure prediction (no MSA), run locally or via the ESM Atlas API; a Claude Science skill.
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.
Enzyme Kinetics (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA
ToolUniverse agent skill that fits Michaelis-Menten kinetics to substrate-velocity data and classifies inhibition mechanism with a Ki estimate.
Evo 2 (Claude Skill)
Claude Skill · Arc Institute · GA · verified: works · security: cleared
Evo 2 genome language model for DNA/RNA/protein sequence generation and variant scoring; local (Hopper GPU) or NVIDIA-hosted; a Claude Science skill.
FinnGen (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Finnish biobank GWAS summary statistics across thousands of endpoints from FinnGen; a source in the Human Genetics connector in Claude Science.
GATK (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs.
GSEApy (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
GSEA and over-representation analysis (ORA) for RNA-seq and proteomics.
GTEx Expression Database (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Query the GTEx Portal for median RNA expression (TPM) across 54 human tissues and eQTLs linking variants to gene expression.
GWAS Catalog (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS.
GWAS Drug Discovery (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that turns GWAS-significant loci into druggable targets and repurposing candidates via fine-mapping, tractability scoring, and drug matching.
GWAS-MCP
MCP server · ZaEyAsa · GA · verified: works · security: caution
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)
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 Liability Evaluation (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA
ToolUniverse agent skill that scores the human safety liability of inhibiting or knocking out a gene across five evidence dimensions.
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.
Ginkgo Cloud Lab (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
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).
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.
HMDB (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping.
HOMER (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER.
Harmony (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Harmony batch correction for scRNA-seq and other omics.
Hashtag Demultiplexing (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Assign pooled single-cell data back to sample of origin from HTO, MULTI-seq or CellPlex tags and call cross-sample doublets
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.
IntAct (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Molecular-interaction evidence from EMBL-EBI’s IntAct database; a source in the Structures & Interactions connector in Claude Science.
JASPAR (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
JASPAR 2024 TF binding profiles via REST API and pyJASPAR.
KEGG Database (REST API) (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: caution
KEGG REST API (academic only).
KEGG Pathway Analysis (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: caution
Guide to KEGG pathway enrichment for DEG results.
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.
LabArchives (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Electronic lab notebook API integration.
LaminDB (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.
LatchBio (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Latch platform for bioinformatics workflows.
Lineage Tracing (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Reconstruct single-cell lineage trees from CRISPR scars, expressed barcodes or mtDNA mutations using Cassiopeia, Startle and CoSpar
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.).
MACS3 (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs.
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.
MOFA+ (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2.
MSA Statistics (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Compute percent identity, conservation scores, gap profiles and substitution-matrix statistics over a multiple alignment with BioPython, and read them correctly
MaxQuant (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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 …
MetaboLights (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
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)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
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)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.
Monarch Initiative (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.
Mouse Phenome Database (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.
MultiQC (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Aggregates QC from 150+ bioinformatics tools into one interactive HTML report.
Multiple Sequence Alignment (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Build multiple sequence alignments with MAFFT, MUSCLE5, Clustal Omega or T-Coffee, choosing the algorithm by dataset size and divergence
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.
NCBI GEO
Claude Skill · SciAgent / MCPmed · GA · verified: works · security: cleared
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)
Claude Skill · SciAgent · GA · verified: works · security: cleared
NCBI Gene via E-utilities: curated records across 1M+ taxa.
OMERO (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Microscopy data management platform.
Omics Analysis Guide (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
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.
Open Targets Plugin
Claude Code Plugin · Open Targets · GA · verified: degraded · security: caution
Official Open Targets MCP plugin giving Claude GraphQL access to target-disease associations, drug evidence, and target-prioritisation scores.
OpenCV (Bio-image) (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Computer vision for bio-image preprocessing, feature detection, real-time microscopy.
Opentrons (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Official Opentrons Protocol API for OT-2 and Flex robots.
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.
PLINK2 (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
GWAS and population genetics tool.
PRIDE (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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)
Claude Skill · K-Dense · GA · verified: works · security: caution
Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.
Pathway Enrichment (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results.
Perturb-seq Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Analyze single-cell CRISPR screens with Pertpy, Mixscape escaper removal, SCEPTRE calibrated testing and E-distance effect sizes
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).
Polars-Bio (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames.
PrimeKG (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
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.
Protocols.io (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
Integration with protocols.io API for managing scientific protocols.
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.
PyImageJ / Fiji (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops.
PyLabRobot (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Vendor-agnostic lab automation framework.
QuickGO (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query EBI QuickGO REST API for GO terms and protein annotations.
RNA Structure Probing (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
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)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
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)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill for rare-disease investigation — Orphanet characterization, HPO phenotypes, causative genes, GenCC validity, ClinVar variants, trials, and repurposing.
ReMap (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.
Reactome (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs.
RegulomeDB (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs …
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.
Rfam (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Non-coding RNA families, covariance models, and alignments from EMBL-EBI’s Rfam; the RNA connector in Claude Science.
Rhea (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Expert-curated biochemical reactions from Rhea (SIB); a source in the Chemistry connector in Claude Science.
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.
SAMtools (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.
STAR (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables.
STRING (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species).
Salmon (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM).
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.
Single-Cell Annotation Guide (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Decision framework for manual marker-based, automated (CellTypist), and reference-based (popV) cell type annotation in scRNA-seq.
SnpEff / SnpSift (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Annotate and filter VCF variants with SnpEff and SnpSift.
Somatic Signatures (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: caution
Extracts and assigns COSMIC v3.4 mutational signatures from somatic VCFs with SigProfiler, MutationalPatterns, MuSiCal or HRDetect to read DNA-damage etiology
Synapse.org Connector
MCP server · Sage Bionetworks · GA · verified: works · security: cleared
Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.
TAD Detection (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Call TAD boundaries from balanced Hi-C matrices with cooltools insulation scores, including the window sweep and boundary-strength ranking
Target Research (ToolUniverse Claude Skill)
Claude Skill · Zitnik Lab (Harvard Medical School) · GA · verified: works · security: cleared
ToolUniverse agent skill that profiles a drug target across nine parallel research paths — expression, pathways, interactions, variants, druggability — into a cited report.
TileDB-VCF (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Efficient storage and retrieval of genomic variant data using TileDB.
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.
UCSC Cell Browser MCP
MCP server · MCPmed · Beta
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)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.
UniBind TF Binding Sites (Claude Skill)
Claude Skill · Google DeepMind · GA · verified: degraded · security: cleared
Query UniBind for experimentally validated transcription-factor binding sites; download BED/FASTA coordinates by species, cell line, or TF.
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.
ViennaRNA (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.
Western Blot Quantification (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods
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.
cBioPortal (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Cancer genomics (TCGA et al.) via cBioPortal REST API.
cBioPortal MCP Server
MCP server · cBioPortal · GA · verified: works · security: caution
Query cancer genomics studies, mutations, and clinical data from cBioPortal; also the Cancer Models connector in Claude Science.
dbSNP (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.
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.
deepTools (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
NGS analysis toolkit.
eQTL Catalogue (Claude Science Connector)
Claude.ai Connector · Anthropic · GA · verified: works · security: cleared
Uniformly processed cis-QTL (eQTL/sQTL) summary statistics from EMBL-EBI’s eQTL Catalogue; a source in the Human Genetics connector in Claude Science.
fastp (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
All-in-one FASTQ QC and adapter trimming.
featureCounts (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Counts RNA-seq reads overlapping GTF gene features.
geniml (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Working with genomic interval data (BED files) for machine learning tasks.
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.
gnomAD (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
GnomAD v4 population variant frequencies via GraphQL API.
gtars (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: caution
High-performance toolkit for genomic interval analysis in Rust with Python bindings.
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.
libSBML (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Build, read, validate, modify SBML biological network models via the libSBML Python API.
muon (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Multi-modal single-cell analysis with muon/MuData.
napari (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Interactive viewer for microscopy.
ncRNA Search (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Find non-coding RNA homologs and assign Rfam families with Infernal covariance models, scoring sequence and secondary structure together
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.
pLannotate (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene).
pacsomatic (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.
popV (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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.
pyOpenMS (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Complete mass spectrometry analysis platform.
pysam (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
Genomic file toolkit.
scATAC Analysis (bioSkills)
Claude Skill · GPTomics bioSkills · GA · verified: works · security: cleared
Process single-cell ATAC-seq with Signac, ArchR or SnapATAC2 — fragment QC, TF-IDF/LSI, consensus peaks and chromVAR motif deviations
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.
scVelo (Claude Skill)
Claude Skill · K-Dense · GA · verified: works · security: cleared
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
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.
scikit-image (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Python image processing for microscopy and bioimage analysis.
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.
sgRNA Design (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
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
Claude Skill · Anthropic · GA · verified: works · security: cleared
scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.
trackpy (Claude Skill)
Claude Skill · SciAgent · GA · verified: works · security: cleared
Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm.
Got feedback on a tool?
Use the tool-feedback Issue Form — pick the tool from a dropdown, describe what happened. A bot replies in-thread shortly; the next daily catalog run incorporates the feedback.