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
Conversational orchestration of 10x Cloud single-cell, immune-profiling, and spatial-transcriptomics analyses.
ARCHS4 (Claude Skill)
Claude Skill · SciAgent · GA
Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples.
AlphaFold MCP Server
MCP server · Augmented Nature · GA
MCP server exposing the EBI AlphaFold Protein Structure Database for structure retrieval, pLDDT analysis, comparison, and PyMOL/ChimeraX export.
AnnData (Claude Skill)
Claude Skill · K-Dense · GA
Claude skill teaching the AnnData annotated-data-matrix format used by Scanpy and scvi-tools for single-cell and other observation/feature matrices.
Anthropic PubMed Connector
MCP server · Anthropic · GA
Anthropic-managed NCBI literature search via PubMed and PubMed Central.
Arboreto (Claude Skill)
Claude Skill · K-Dense · GA
Claude skill for gene-regulatory-network inference with Arboreto — GRNBoost2 / GENIE3 tree-based regression over bulk or single-cell expression, distributed via Dask.
BCFtools (Claude Skill)
Claude Skill · SciAgent · GA
CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats.
BEDTools (Claude Skill)
Claude Skill · SciAgent · GA
Genomic interval ops on BED/BAM/GFF/VCF.
BGPT Paper Search (Claude Skill)
Claude Skill · K-Dense · GA
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
BRENDA (Claude Skill)
Claude Skill · SciAgent · GA
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
Fast short-read DNA aligner for WGS/WES/ChIP-seq.
Bakta (Claude Skill)
Claude Skill · SciAgent · GA
Annotate bacterial and archaeal genomes and plasmids with Bakta’s Prodigal/HMM/diamond pipeline.
Benchling (Claude Skill)
Claude Skill · K-Dense · GA
Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.
BioContextAI Knowledgebase MCP
MCP server · BioContextAI · GA
Read-only MCP that unifies 14+ biomedical databases (Antibody Registry, UniProt, STRING, AlphaFold, KEGG, Open Targets) for immune and protein-context queries.
BioMCP
MCP server · GenomOncology · GA
Unified biomedical lookup across PubMed, ClinicalTrials.gov, MyVariant, and OpenFDA.
BioPython (Claude Skill)
Claude Skill · K-Dense · GA
Comprehensive molecular biology toolkit.
BioRender Connector
MCP server · BioRender · GA
Scientific-figure assembly from the 50,000+ BioRender icon and template library.
BioServices (Claude Skill)
Claude Skill · K-Dense · GA
Unified Python interface to 40+ bioinformatics services.
Biomni (Claude Skill)
Claude Skill · Stanford SNAP Lab · GA
General-purpose biomedical AI agent that plans and runs multi-step research workflows across genomics, drug discovery, and clinical analysis.
Bulk RNA-seq (Claude Skill)
Claude Skill · K-Dense · GA
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 …
CNVkit (Claude Skill)
Claude Skill · SciAgent · GA
Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).
COBRApy (Claude Skill)
Claude Skill · K-Dense · GA
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
Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.
CellChat (Claude Skill)
Claude Skill · SciAgent · GA
Infer and visualize intercellular communication from scRNA-seq with CellChat (R).
CellRank-MCP
MCP server · scmcphub · GA
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
Automated scRNA-seq cell type annotation via pre-trained logistic regression.
Cellpose (Claude Skill)
Claude Skill · SciAgent · GA
DL cell/nucleus segmentation for fluorescence and brightfield microscopy.
Cellxgene Census (Claude Skill)
Claude Skill · K-Dense · GA
Claude skill for querying the CZ CELLxGENE Discover census — 50M+ standardized single-cell observations across 1,000+ datasets via TileDB-SOMA, with AnnData / Scanpy integration.
ClinVar (Claude Skill)
Claude Skill · SciAgent · GA
Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations.
Composer
Plugin · Scripps AI Enablement · Beta
Turns a plain-language scientific problem into a grounded, runnable Claude solution composed from this catalog, reusing recipes and recommending autonomous systems.
Consensus Plugin
Claude Code Plugin · Consensus · GA
Consensus.app MCP plugin bringing AI-powered scientific literature search and evidence synthesis into Claude across all research areas.
DESeq2 (R/Bioconductor) (Claude Skill)
Claude Skill · SciAgent · GA
Bulk RNA-seq DE with R/Bioconductor DESeq2.
DNAnexus (Claude Skill)
Claude Skill · K-Dense · GA
DNAnexus cloud genomics platform.
Database Lookup (Claude Skill)
Claude Skill · K-Dense · GA
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs.
DepMap (Claude Skill)
Claude Skill · K-Dense · GA
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.
ENA (Claude Skill)
Claude Skill · SciAgent · GA
ENA REST API for sequences, reads, assemblies, and annotations.
ENCODE (Claude Skill)
Claude Skill · SciAgent · GA
ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types.
ETE Toolkit (Claude Skill)
Claude Skill · K-Dense · GA
Phylogenetic tree toolkit (ETE).
Ensembl MCP Server
MCP server · effieklimi · GA
MCP server over the Ensembl REST API for gene/transcript lookup, sequence retrieval, variant consequences, comparative genomics, and assembly lift-over.
GATK (Claude Skill)
Claude Skill · SciAgent · GA
GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs.
GSEApy (Claude Skill)
Claude Skill · SciAgent · GA
GSEA and over-representation analysis (ORA) for RNA-seq and proteomics.
GWAS Catalog (Claude Skill)
Claude Skill · SciAgent · GA
NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS.
Ginkgo Cloud Lab (Claude Skill)
Claude Skill · K-Dense · GA
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).
HMDB (Claude Skill)
Claude Skill · SciAgent · GA
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
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER.
Harmony (Claude Skill)
Claude Skill · SciAgent · GA
Harmony batch correction for scRNA-seq and other omics.
Human Protein Atlas MCP Server
MCP server · Augmented Nature · GA
Query the Human Protein Atlas — tissue/blood/brain expression, subcellular localization, cancer markers, and antibody validation/staining data.
Hypothesis Generation (Claude Skill)
Claude Skill · K-Dense · GA
Structured hypothesis formulation from observations.
JASPAR (Claude Skill)
Claude Skill · SciAgent · GA
JASPAR 2024 TF binding profiles via REST API and pyJASPAR.
KEGG Database (REST API) (Claude Skill)
Claude Skill · SciAgent · GA
KEGG REST API (academic only).
KEGG Pathway Analysis (Claude Skill)
Claude Skill · SciAgent · GA
Guide to KEGG pathway enrichment for DEG results.
LIANA-MCP
MCP server · scmcphub · GA
MCP server wrapping LIANA so Claude can infer and plot cell-cell communication from single-cell data in natural language.
LabArchives (Claude Skill)
Claude Skill · K-Dense · GA
Electronic lab notebook API integration.
LaminDB (Claude Skill)
Claude Skill · K-Dense · GA
Working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models.
LatchBio (Claude Skill)
Claude Skill · K-Dense · GA
Latch platform for bioinformatics workflows.
Literature Review (Claude Skill)
Claude Skill · K-Dense · GA
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
MACS3 (Claude Skill)
Claude Skill · SciAgent · GA
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs.
MOFA+ (Claude Skill)
Claude Skill · SciAgent · GA
Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2.
MaxQuant (Claude Skill)
Claude Skill · SciAgent · GA
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 …
Metabolomics Workbench (Claude Skill)
Claude Skill · SciAgent · GA
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
Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.
Mouse Phenome Database (Claude Skill)
Claude Skill · SciAgent · GA
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.
MultiQC (Claude Skill)
Claude Skill · SciAgent · GA
Aggregates QC from 150+ bioinformatics tools into one interactive HTML report.
NCBI GEO (Claude Skill)
Claude Skill · SciAgent · GA
NCBI GEO access via GEOparse and E-utilities.
NCBI Gene (Claude Skill)
Claude Skill · SciAgent · GA
NCBI Gene via E-utilities: curated records across 1M+ taxa.
OMERO (Claude Skill)
Claude Skill · K-Dense · GA
Microscopy data management platform.
Omics Analysis Guide (Claude Skill)
Claude Skill · SciAgent · GA
Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods
Open Targets Plugin
Claude Code Plugin · Open Targets · GA
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
Computer vision for bio-image preprocessing, feature detection, real-time microscopy.
Opentrons (Claude Skill)
Claude Skill · K-Dense · GA
Official Opentrons Protocol API for OT-2 and Flex robots.
PLINK2 (Claude Skill)
Claude Skill · SciAgent · GA
GWAS and population genetics tool.
PRIDE (Claude Skill)
Claude Skill · SciAgent · GA
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
Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles.
Pathway Enrichment (Claude Skill)
Claude Skill · K-Dense · GA
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results.
Phylogenetics (Claude Skill)
Claude Skill · K-Dense · GA
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML).
Polars-Bio (Claude Skill)
Claude Skill · K-Dense · GA
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames.
PrimeKG (Claude Skill)
Claude Skill · K-Dense · GA
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
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka’s BLAST/HMM pipeline.
Protocols.io (Claude Skill)
Claude Skill · K-Dense · GA
Integration with protocols.io API for managing scientific protocols.
PyDESeq2 (Claude Skill)
Claude Skill · K-Dense · GA
Claude skill for bulk RNA-seq differential expression with PyDESeq2 — size factors, dispersion, Wald / LRT testing, BH-adjusted p-values.
PyImageJ / Fiji (Claude Skill)
Claude Skill · SciAgent · GA
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
Vendor-agnostic lab automation framework.
QuickGO (Claude Skill)
Claude Skill · SciAgent · GA
Query EBI QuickGO REST API for GO terms and protein annotations.
ReMap (Claude Skill)
Claude Skill · SciAgent · GA
Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.
Reactome (Claude Skill)
Claude Skill · SciAgent · GA
Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs.
RegulomeDB (Claude Skill)
Claude Skill · SciAgent · GA
Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs …
Roary (Claude Skill)
Claude Skill · SciAgent · GA
Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary’s CD-HIT + BLAST + MCL clustering pipeline.
SAMtools (Claude Skill)
Claude Skill · SciAgent · GA
CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.
STAR (Claude Skill)
Claude Skill · SciAgent · GA
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables.
STRING (Claude Skill)
Claude Skill · SciAgent · GA
Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species).
Salmon (Claude Skill)
Claude Skill · SciAgent · GA
Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM).
Scanpy-MCP
MCP server · scmcphub · GA
MCP server wrapping Scanpy so Claude can run end-to-end single-cell RNA-seq analyses (QC, clustering, DE, plotting) from natural language.
Scholar Gateway Connector (Wiley)
MCP server · Wiley · Beta
Wiley remote connector for peer-reviewed scholarly content — 3M+ articles, 300+ Life Sciences journals.
Scientific Brainstorming (Claude Skill)
Claude Skill · K-Dense · GA
Creative research ideation and exploration.
Scientific Critical Thinking (Claude Skill)
Claude Skill · K-Dense · GA
Evaluate scientific claims and evidence quality.
Single-Cell Annotation Guide (Claude Skill)
Claude Skill · SciAgent · GA
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
Annotate and filter VCF variants with SnpEff and SnpSift.
Synapse.org Connector
MCP server · Sage Bionetworks · GA
Discovery and metadata retrieval across Synapse-hosted biomedical datasets and consortium projects.
TileDB-VCF (Claude Skill)
Claude Skill · K-Dense · GA
Efficient storage and retrieval of genomic variant data using TileDB.
ToolUniverse
MCP server · Zitnik Lab (Harvard Medical School) · MIT Lincoln Laboratory · GA
Harvard / MIT MCP server bundling 600+ vetted scientific tools — literature, chemistry, omics, clinical trials — for AI-scientist-style hypothesis exploration.
UCSC Genome Browser (Claude Skill)
Claude Skill · SciAgent · GA
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.
UniProt MCP Server
MCP server · Augmented Nature · GA
MCP server giving Claude 26 tools over the UniProt REST API for protein search, domains, orthologs, PTMs, pathways, and multi-format export.
ViennaRNA (Claude Skill)
Claude Skill · SciAgent · GA
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
Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods
bio-research (Claude Code Plugin)
Claude Code Plugin · Anthropic · GA
Umbrella plugin bundling 5 analysis skills and ~10 MCP connectors (PubMed, BioRender, ChEMBL, Synapse, Wiley, Open Targets, Benchling, etc.) for preclinical R&D.
cBioPortal (Claude Skill)
Claude Skill · SciAgent · GA
Cancer genomics (TCGA et al.) via cBioPortal REST API.
dbSNP (Claude Skill)
Claude Skill · SciAgent · GA
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
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
NGS analysis toolkit.
fastp (Claude Skill)
Claude Skill · SciAgent · GA
All-in-one FASTQ QC and adapter trimming.
featureCounts (Claude Skill)
Claude Skill · SciAgent · GA
Counts RNA-seq reads overlapping GTF gene features.
geniml (Claude Skill)
Claude Skill · K-Dense · GA
Working with genomic interval data (BED files) for machine learning tasks.
gget (Claude Skill)
Claude Skill · K-Dense · GA
Claude skill wrapping the gget command-line / Python tool for fast unified queries against Ensembl, UniProt, NCBI, PDB, COSMIC, and other genomics databases.
gnomAD (Claude Skill)
Claude Skill · SciAgent · GA
GnomAD v4 population variant frequencies via GraphQL API.
gtars (Claude Skill)
Claude Skill · K-Dense · GA
High-performance toolkit for genomic interval analysis in Rust with Python bindings.
instrument-data-to-allotrope
Claude Skill · Anthropic · GA
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
Build, read, validate, modify SBML biological network models via the libSBML Python API.
muon (Claude Skill)
Claude Skill · SciAgent · GA
Multi-modal single-cell analysis with muon/MuData.
napari (Claude Skill)
Claude Skill · SciAgent · GA
Interactive viewer for microscopy.
nextflow-development
Claude Skill · Anthropic · GA
Runs nf-core rnaseq, sarek, and atacseq pipelines on local FASTQ or GEO/SRA inputs.
pLannotate (Claude Skill)
Claude Skill · SciAgent · GA
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
Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.
popV (Claude Skill)
Claude Skill · SciAgent · GA
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
Complete mass spectrometry analysis platform.
pysam (Claude Skill)
Claude Skill · K-Dense · GA
Genomic file toolkit.
scVelo (Claude Skill)
Claude Skill · K-Dense · GA
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
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
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
Python image processing for microscopy and bioimage analysis.
scvi-tools
Claude Skill · Anthropic · GA
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
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
scverse MAD-based QC for .h5ad and 10x .h5 single-cell RNA-seq inputs.
trackpy (Claude Skill)
Claude Skill · SciAgent · GA
Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm.
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