tooluniverse

Plugin tooluniverse from marketplace tooluniverse in mims-harvard/ToolUniverse. Commands read from the repo's manifest — 3 days ago.

Skills (163)

• setup-tooluniverse

  Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 14 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cl

• tooluniverse-acmg-variant-classification

  Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation

• tooluniverse-admet-prediction

  Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, SwissADME drug-likeness, PubChemTox experimental toxicity, ChEMBL clinical data, Lipinski rule-of-five, and CYP interaction data. Use for drug-likeness asse

• tooluniverse-adverse-event-detection

  Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, regulatory sub

• tooluniverse-adverse-outcome-pathway

  Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characteriza

• tooluniverse-aging-senescence

  Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, a

• tooluniverse-antibody-engineering

  Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and m

• tooluniverse-antigravity-plugin

  Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy), the "agy plugin install <path>" flow, the

• tooluniverse-binder-discovery

  Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target

• tooluniverse-bioinformatics-resource-discovery

  Discover which bioinformatics software tool, biomedical REST API, R/Bioconductor package, CRAN package, or training material exists for a task, before writing analysis code or building a pipeline. Covers ELIXIR bio.tools (30,000+ software tools/databases by keyword, EDAM topic, or EDAM operation), S

• tooluniverse-biomedical-fact-lookup

  Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to <database>' (DisGeNet, OMIM, MSigDB, miRDB, GTRD,

• tooluniverse-cancer-classification

  Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring

• tooluniverse-cancer-genomics-tcga

  TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics integration. Use for TCGA-BRCA-style cohort studies, mutation prevalence by cancer type, survival-by-mutation analysis, and pan-cancer driver discove

• tooluniverse-cancer-variant-interpretation

  Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical evidence tier (CIViC, OncoKB), therapeutic options (FDA-approved + investigational), resistance mechanisms, prognosis, and matching clinical

• tooluniverse-cell-line-profiling

  Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for study

• tooluniverse-chemical-compound-retrieval

  Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing

• tooluniverse-chemical-safety

  Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, and exposure-context analysis. Use for chemical hazard identification, occupational/consumer-product toxicity, dose-response evaluation, and a

• tooluniverse-chemical-sourcing

  Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mcule. Compares pricing, availability, and identifies purchasable analogs when an exact compound is not in stock. Use for chemical procurement, virtual lib

• tooluniverse-claude-code-plugin

  Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 2,700+ scientific tools, 160+ research skills, slash commands, hooks, and the research agent. Use for first-time plugin install, troubleshooting plugin not loading, verifying MCP server connection, listing API key req

• tooluniverse-clinical-data-integration

  End-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharmacogenomic biomarkers, clinical trial data, and published literature. Use for regulatory drug safety reviews, comprehensive pharmacovigilance reports, label-vs-real-world AE comparison

• tooluniverse-clinical-guidelines

  Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL European societies, and US specialty associations. Use for evidence-graded treatment recommendations, dosing protocols, screening guidance, an

• tooluniverse-clinical-risk-scoring

  Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the scenario, gather inputs, run the deterministic calculator tool, and read the result against an interpretation table. Covers CHA2DS2-VASc (AF stroke risk), H

• tooluniverse-clinical-terminology-lookup

  Fast autocomplete/normalization lookups against the NLM Clinical Table Search Service — resolve a partial or informal drug name to its RxTerms display name and RxCUI, autocomplete a health condition or problem-list entry to its formal name and ICD-10-CM/ICD-9-CM codes, normalize a disease mention to

• tooluniverse-clinical-trial-design

  Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and approval-pathway analysis. Use for trial

• tooluniverse-clinical-trial-matching

  AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) and clinical state into ranked clinical-trial recommendations with evidence tiers. Searches ClinicalTrials.gov, the EU CTIS register (Europea

• tooluniverse-clinical-trial-protocol

  Generate a full clinical trial protocol document (ICH E6(R2)/FDA-style) for a drug or medical device, including background, objectives/endpoints, study design, population/eligibility, intervention details, assessment schedule, statistical analysis plan with sample-size justification, safety monitori

• tooluniverse-comparative-genomics

  Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic ge

• tooluniverse-computational-biophysics

  Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology (LD50, NOAEL), population genetics (Hardy-Weinberg, Fst), enzyme kinetics (Michaelis-Menten), thermodynamics. Use for first-principles quantitati

• tooluniverse-connect

  How to use ToolUniverse Connect (connect.aiscientist.tools), the hosted ToolUniverse service, and when to use it instead of ToolUniverse installed on this computer. Use when the user asks how to use ToolUniverse or ToolUniverse Connect, how to connect Claude, Claude Code or Codex, whether to use the

• tooluniverse-crispr-screen-analysis

  Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Use for genome-wide essentiality screens, synthetic-lethality discovery, dropout vs positive-selection screen analysis, target identification,

• tooluniverse-custom-tool

  Add custom local tools to ToolUniverse alongside the 2,700+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contri

• tooluniverse-data-integration-analysis

  Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findin

• tooluniverse-data-wrangling

  Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need bulk records. Use for VCF/h5ad/BAM/SDF/GCT parsing, multi-step API workflows (search to filter to download to parse), thousands of records at o

• tooluniverse-database-logins

  Help the user add the login (API key) that a ToolUniverse tool needs for a database such as NCBI/PubMed, OMIM, DisGeNET, UMLS or OpenAlex, without the key ever passing through the chat. Explains which login unlocks what, where to get it, where to paste it, and retries the tool. Use when a tool says

• tooluniverse-dataset-discovery

  Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional, observational vs experimental, single-cohort vs multi-cohort). Use when the user asks 'find data about X', 'where can I get data on Y', or needs a spec

• tooluniverse-diagnostic-test-evaluation

  Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the optimal cutoff (Youden) for a continuous biomarker; and post-test probability via Bayes. Use when you have test results vs a gold standard (binary 2x2, or

• tooluniverse-disease-research

  Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing candidates), clinical trials, epidemiology (prevalence, incidence), and phenotypes (HPO). Use for full disease overviews, comprehensive dise

• tooluniverse-dose-response

  Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response data (enzyme/cell assays, drug screening, agonist/antagonist pharmacology). Fits the 4-parameter logistic (Hill sigmoidal) model. Use when you

• tooluniverse-drug-drug-interaction

  Assess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic synergy/antagonism, clinical significance scoring, and management recommendations. Use for polypharmacy review, prescribing decision support, and safety a

• tooluniverse-drug-mechanism-research

  Trace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect → clinical outcome. Uses DrugBank, ChEMBL, KEGG, Reactome, STRING. Use for understanding how a drug works, identifying off-target effects, mechanism-based combination therapy design, a

• tooluniverse-drug-regulatory

  Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulato

• tooluniverse-drug-repurposing

  Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechanism rationale, clinical-trial precedent, and patent/regulatory feasibility. Use for hypothesis-generating repurposing for orphan diseases, fi

• tooluniverse-drug-research

  Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researc

• tooluniverse-drug-synergy

  Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-dr

• tooluniverse-drug-target-validation

  Quantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite Target Validation Score (0-100) and GO/NO-GO recommendation. Use for go/no-go decisions on a target before commit-to-medchem, target priorit

• tooluniverse-ecology-biodiversity

  Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion biology, conservation prioritization, and ecol

• tooluniverse-electron-microscopy

  Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Use for finding 3D structural data on a protein/complex, comparing experimental EM resolution to AlphaFo

• tooluniverse-enzyme-design

  De novo enzyme design by catalytic-motif scaffolding — build a transition-state motif, generate scaffolds with AlphaProtein Novo, fold every mechanistic state, and triage with mechanism-inspired filters (catalytic geometry, multi-state H-bonds, multi-resequence backbone scoring). Use for designing e

• tooluniverse-enzyme-kinetics

  Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki). Fits the MM equation by nonlinear regression (and reports Line

• tooluniverse-epidemiological-analysis

  End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statistical report. Covers cohort/case-control/cross-sectional design, regression with confounders, propensity scoring, sensitivity analysis. Writes Python code

• tooluniverse-epigenomics-chromatin

  Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas. Use for chromatin-state-by-tissue queries, TF-binding-by-region, regulatory landscape mapping, and ENCODE-cCRE annotations. For DNA methylation use tooluniver

• tooluniverse-epigenomics

  Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam computation with ToolUniverse annotation tools.

• tooluniverse-expression-data-retrieval

  Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray datasets by organism/tissue/condition, comparing across studies (case-control, time-series, dose-response), and assessing dataset suitabili

• tooluniverse-fastq-qc

  FASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, interpret per-base sequence quality, per-base N content, adapter content, overrepresented sequences, sequence duplication and GC content, and decide whether

• tooluniverse-functional-genomics-screens

  Interpret hits from CRISPR-KO/CRISPRi/shRNA screens by integrating DepMap essentiality, gnomAD constraint scores, pathway context (Reactome, STRING), druggability (DGIdb), and clinical evidence (CIViC, COSMIC). Use for screen-hit prioritization, essentiality ranking, and turning a list of screen hit

• tooluniverse-gene-disease-association

  Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet, Gene2Phenotype (G2P). Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak). Use for 'which diseases is gene X associa

• tooluniverse-gene-enrichment

  Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA, plus g:Profiler for enrichment/ID conversion/ortholog mapping/SNP-to-gene annotation. Use for interpreting DEG lists, screen hit l

• tooluniverse-gene-liability

  Evaluate the human safety liability of knocking down, knocking out, degrading, or pharmacologically inhibiting a gene. Use for gene safety scoring, on-target toxicity assessment, essentiality and genetic-constraint review, critical-organ expression analysis, or deciding whether a target needs partia

• tooluniverse-gene-regulatory-networks

  Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout/overexpression). Use for 'which TF regulates gene X', 'which genes does TF Y target', regulatory pathway reconstruction. Distinguishes direct (binding)

• tooluniverse-glycobiology

  Glycobiology and glycomics research using GlyGen — glycan structure lookup by GlyTouCan accession, glycan search by mass/monosaccharide-count/type, glycoprotein glycosylation profiles by UniProt accession, glycosylation-site-level detail (position, flanking sequence, attached glycan, co-located SNVs

• tooluniverse-gpcr-structural-pharmacology

  GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric v

• tooluniverse-gwas-drug-discovery

  Transform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable proteins via DGIdb/OpenTargets, then to existing drugs via ChEMBL. Use for GWAS-to-target hypothesis generation, druggable-fraction analysis

• tooluniverse-gwas-finemapping

  Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal variants and target genes — distinct from positional 'nearest gene' which is often wrong. Use for prioritizing causal variants at GWAS hits, comparing fin

• tooluniverse-gwas-snp-interpretation

  Interpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gnomAD frequency. Use for 'what does this SNP do', SNP-to-mechanism tracing, and resolving lead-SNP-vs-causal-variant ambiguity. Always consid

• tooluniverse-gwas-study-explorer

  Compare GWAS studies, perform meta-analyses across cohorts, and assess signal replication. Uses GWAS Catalog metadata, study-level statistics, and cross-cohort comparison. Use for evaluating GWAS reproducibility for a trait, meta-analysis sample size and effect-size aggregation, and detecting study

• tooluniverse-gwas-trait-to-gene

  Discover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, and distance evidence. Use for trait-to-gene mapping, drug-target hypothesis generation from GWAS, and replacing the 'nearest gene' heuristic with multi-e

• tooluniverse-hla-immunogenomics

  HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer immunotherapy. Uses IMGT (HLA polymorphism), IEDB (epitope-MHC binding), UniProt (annotation), DGIdb (druggability). Use for HLA typing/imputation review, vaccine HLA coverage, and imm

• tooluniverse-image-analysis

  Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, im

• tooluniverse-immune-repertoire-analysis

  TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification. Use for adaptive immune response characterization, post-treatment immune monitoring, antigen-specific clone tracking, and clonal-expansion

• tooluniverse-immunology

  Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoimmune disease genetics, vaccine epitope mapping. Uses IEDB, IMGT, SAbDab, UniProt. Use for adaptive immunity questions, immune response analysis, antibody/TCR/BCR characterization, imm

• tooluniverse-immunotherapy-response-prediction

  Predict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression, HLA status, and immune-related gene expression. Outputs ICI Response Score with drug-specific recommendations and resistance-risk assessme

• tooluniverse-infectious-disease
• tooluniverse-inorganic-physical-chemistry
• tooluniverse-install-skills
• tooluniverse-kegg-disease-drug
• tooluniverse-lab-data-standardization
• tooluniverse-lab-protocols
• tooluniverse-lipidomics
• tooluniverse-literature-deep-research
• tooluniverse-medical-imaging-radiology
• tooluniverse-mendelian-randomization
• tooluniverse-meta-analysis
• tooluniverse-metabolomics-analysis
• tooluniverse-metabolomics-pathway
• tooluniverse-metabolomics
• tooluniverse-metagenomics-analysis
• tooluniverse-microbial-genome-characterization
• tooluniverse-microbiome-research
• tooluniverse-ml-inference-utility
• tooluniverse-model-organism-genetics
• tooluniverse-molecular-cloning
• tooluniverse-multi-omics-integration
• tooluniverse-multiomic-disease-characterization
• tooluniverse-natural-product-dereplication
• tooluniverse-network-pharmacology
• tooluniverse-neuroscience
• tooluniverse-neurosynth-meta-analysis
• tooluniverse-nfcore-pipelines
• tooluniverse-nih-funding-landscape
• tooluniverse-noncoding-rna
• tooluniverse-nutrition-food-composition
• tooluniverse-organic-chemistry
• tooluniverse-pathway-disease-genetics
• tooluniverse-peptide-target-deorphanization
• tooluniverse-pharmacogenomics
• tooluniverse-pharmacokinetics
• tooluniverse-pharmacovigilance
• tooluniverse-phewas
• tooluniverse-phylogenetics
• tooluniverse-plant-genomics
• tooluniverse-polygenic-risk-score
• tooluniverse-population-genetics-1000genomes
• tooluniverse-population-genetics
• tooluniverse-precision-medicine-stratification
• tooluniverse-precision-oncology
• tooluniverse-primer-design
• tooluniverse-product-safety-surveillance
• tooluniverse-protein-design-campaign
• tooluniverse-protein-interactions
• tooluniverse-protein-lof-mechanism
• tooluniverse-protein-modification-analysis
• tooluniverse-protein-sae-variant-interpretation
• tooluniverse-protein-structural-annotation-pdb
• tooluniverse-protein-structure-prediction
• tooluniverse-protein-structure-retrieval
• tooluniverse-protein-therapeutic-design
• tooluniverse-proteomics-analysis
• tooluniverse-proteomics-data-retrieval
• tooluniverse-publish-tool
• tooluniverse-rare-disease-diagnosis
• tooluniverse-rare-disease-genomics
• tooluniverse-regulatory-genomics
• tooluniverse-regulatory-variant-analysis
• tooluniverse-residue-functional-mechanism-interpretation
• tooluniverse-rnaseq-deseq2
• tooluniverse-scientific-peer-review
• tooluniverse-scientific-problem-selection
• tooluniverse-scvi-tools
• tooluniverse-sdk
• tooluniverse-self-review
• tooluniverse-sequence-analysis
• tooluniverse-sequence-retrieval
• tooluniverse-share-computer
• tooluniverse-single-cell
• tooluniverse-small-molecule-discovery
• tooluniverse-spatial-omics-analysis
• tooluniverse-spatial-transcriptomics
• tooluniverse-statistical-modeling
• tooluniverse-stem-cell-organoid
• tooluniverse-structural-proteomics
• tooluniverse-structural-variant-analysis
• tooluniverse-synthetic-biology-parts
• tooluniverse-systems-biology
• tooluniverse-target-research
• tooluniverse-toxicology
• tooluniverse-use-shared-computer
• tooluniverse-vaccine-design
• tooluniverse-variant-analysis
• tooluniverse-variant-functional-annotation
• tooluniverse-variant-interpretation
• tooluniverse-variant-predictor-dms-validation
• tooluniverse-variant-to-mechanism
• tooluniverse

Slash commands (8)

• /tooluniverse:compare

  Side-by-side comparison of N items (drugs, targets, diseases, variants, trials, etc.) with a domain-appropriate column set, structured tabular output, and per-cell source citation. Use when the user wants to evaluate alternatives, not when they want a profile of a single item. Enforces the compariso

• /tooluniverse:cross-validate

  Take a specific scientific claim and confirm or refute it across 3+ independent databases, then report concordance. Use before publishing, citing, or acting on a fact when you want to know how strongly it's supported. Forces multi-source verification that the agent doesn't naturally enforce.

• /tooluniverse:literature-sweep

  Run a graded mini-review on a topic across many literature sources, adaptively chosen by domain — a core multi-field set (PubMed, EuropePMC, OpenAlex, Semantic Scholar) plus domain-specific indexes (ArXiv/DBLP for CS, InspireHEP for physics, PubTator/PMC/clinical guidelines for biomedical, Crossref/

• /tooluniverse:research

  Conduct a multi-database scientific research investigation inline in the current chat. Same operating discipline as the /tooluniverse:researcher agent (look up specific claims, cross-validate, honest INDETERMINATE) — but runs in this conversation so you can watch each step, follow up, and refine, in

• /tooluniverse:self-review

  Review current or supplied work against the user's actual goal, report evidence-backed strengths, gaps, risks, and fixes, and give a plain-language completion verdict. Qualitative by default; only score or grade when explicitly requested.

• /tooluniverse:setup-keys

  Set up ToolUniverse API keys. Opens a graphical setup page (or guides you in chat) listing every key tools can use, with registration links, and saves them permanently to a .env that the MCP server, CLI, and SDK all read. Use when a tool reports a missing API key or when first configuring ToolUniver

• /tooluniverse:translate-id

  Resolve an identifier across all relevant namespaces (HGNC symbol, Ensembl, UniProt, NCBI Gene ID, RefSeq, MGI, OMIM, ChEMBL, PubChem, etc.). Detects the input namespace automatically, picks the right resolver tool, and returns a complete cross-reference table. Use when you have an ID in one namespa

• /tooluniverse:verify-references

  Check whether cited references are real and accurately described — confirms each citation actually exists and that its title/authors/year/journal/DOI match what's claimed, using independent databases (Crossref, DataCite, PubMed, OpenAlex, Semantic Scholar, EuropePMC, plus domain-specific sources lik

Subagents (1)

• researcher

  Autonomous scientific research agent with access to 1000+ databases. Use for complex research questions that require searching multiple databases, analyzing data, and synthesizing findings.

MCP servers (1)

• tooluniverse

  runs: uvx tooluniverse

Hooks (2)

• SessionStart

  if [ ! -f ~/.claude/.tooluniverse-plugin-cleanup-done ] && ls ~/.claude/skills/tooluniverse-* 1>/dev/null 2>&1; then rm -rf ~/.claude/skills/tooluniverse-* ~/.claude/skills/create-tooluniverse-skill ~

• SessionStart

  command -v uvx >/dev/null 2>&1 || echo 'ToolUniverse: uv/uvx was not found, so the tooluniverse MCP server cannot start and its tools will be unavailable. Install uv with: curl -LsSf https://astral.s

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