mims-harvard-tooluniverse

Plugin mims-harvard-tooluniverse from marketplace cascade-data-analytics in joshuarweaver/cascade-data-analytics. Commands read from the repo's manifest — 1 month ago.

Skills (186)

• 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-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 1000+ scientific tools, 120+ 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 requ

• 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-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-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-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 1000+ 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 contrib

• 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-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-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. 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 associated with' or 'which ge

• tooluniverse-gene-enrichment

  Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA. Use for interpreting DEG lists, screen hit lists, or any gene-list-to-pathways query. Includes simplify-cutoff handling and union-

• 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-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

  Rapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases (ChEMBL, DGIdb), and literature surveillance (PubMed/EuropePMC). Use for emerging-pathogen profiling, antiviral candidate identification, a

• tooluniverse-inorganic-physical-chemistry

  Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic properties, electronic structure. Use for unit cell volume calculations, coordination geometry, materials property estimation, and inorganic-mechanism reason

• tooluniverse-install-skills

  Detect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any missing skills if none found. Use when the plugin's research skills aren't loading, when migrating between clients, or when verifying a skill i

• tooluniverse-kegg-disease-drug

  KEGG-based disease-drug-variant network research. Connects diseases to causal genes, drugs to molecular targets, and variants to pathways using KEGG's editorially curated databases (KEGG Disease, Drug, Network, Variant, Pathway). Use for drug repurposing via shared pathways, mechanistic disease-gene

• tooluniverse-lipidomics

  Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways (sphingolipid, eicosanoid, steroid, fatty acid), and PubChem chemical info. Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease a

• tooluniverse-literature-deep-research

  Deep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware searches, grades evidence T1-T4, and produces structured reports. Use for systematic literature review, meta-analysis evidence collection, and detailed an

• tooluniverse-mendelian-randomization

  Mendelian randomization (MR) causal inference — does an exposure, risk factor, or biomarker CAUSALLY affect a disease/outcome, using genetic variants as instrumental variables (IEU OpenGWAS / EpiGraphDB MR-EvE). Use this whenever the user asks if X causes Y, whether an observational association is a

• tooluniverse-meta-analysis

  Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean differences, correlations, GWAS betas) with fixed- or random-effects models, quantify heterogeneity (Q, I², τ²), and build a forest plot. Use when you have results from MULTIPLE studi

• tooluniverse-metabolomics-analysis

  Analyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and pathway interpretation. Use for processing mass-spec metabolomics output, normalization choice, untargeted metabolomics workflows, and integrating with o

• tooluniverse-metabolomics-pathway

  Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaCyc), disease associations, enzyme/gene linkage. Use for metabolite-to-pathway-to-disease connections, BridgeDb-based ID conversion, and integrating metabolomics with gene-level pathwa

• tooluniverse-metabolomics

  Metabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. Use for annotating mass-spec features to known metabolites, finding metabolomics studies of a disease, and structured metabolomics research reports with m

• tooluniverse-metagenomics-analysis

  Microbiome and metagenomics analysis using MGnify, GTDB taxonomy, ENA sequencing data, and EuropePMC literature. Covers taxonomic classification, genome quality assessment, biome-clinical phenotype linkage, and pathway interpretation. Use for amplicon/shotgun metagenomics study analysis.

• tooluniverse-microbial-genome-characterization

  Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50

• tooluniverse-microbiome-research

  Microbiome research using MGnify, GTDB, ENA, OLS (ENVO biomes), and EuropePMC. Covers study discovery, taxonomic profiling, host-microbe interaction analysis, and biome-by-condition queries. Use for microbiome study selection, organism-environment associations, and clinical-microbiome literature rev

• tooluniverse-model-organism-genetics

  Cross-species genetic analysis using model organism databases (MGI mouse, ZFIN zebrafish, FlyBase fruit fly, WormBase worm, SGD yeast, RGD rat, GBIF taxonomy). Maps human genes to orthologs, retrieves phenotype/expression/functional data, assesses gene function conservation, and identifies the best

• tooluniverse-molecular-cloning

  Molecular cloning, in both directions. DESIGN — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI / Esp3I / BsmBI / SapI design with unique 4-bp fusion overhangs). ANALYSIS — work out what an existing reaction produces: given input

• tooluniverse-multi-omics-integration
• tooluniverse-multiomic-disease-characterization
• tooluniverse-natural-product-dereplication
• tooluniverse-network-pharmacology
• tooluniverse-neuroscience
• tooluniverse-nih-funding-landscape
• tooluniverse-noncoding-rna
• 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-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-rare-disease-diagnosis
• tooluniverse-rare-disease-genomics
• tooluniverse-regulatory-genomics
• tooluniverse-regulatory-variant-analysis
• tooluniverse-residue-functional-mechanism-interpretation
• tooluniverse-rnaseq-deseq2
• tooluniverse-sdk
• tooluniverse-self-review
• tooluniverse-sequence-analysis
• tooluniverse-sequence-retrieval
• 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-systems-biology
• tooluniverse-target-research
• tooluniverse-toxicology
• tooluniverse-vaccine-design
• tooluniverse-variant-analysis
• tooluniverse-variant-functional-annotation
• tooluniverse-variant-interpretation
• tooluniverse-variant-predictor-dms-validation
• tooluniverse-variant-to-mechanism
• tooluniverse
• tooluniverse-codex-plugin
• create-tooluniverse-skill
• skill_template
• devtu-auto-discover-apis
• devtu-benchmark-harness
• devtu-code-optimization
• devtu-create-tool
• devtu-docs-quality
• devtu-fix-tool
• devtu-github
• devtu-optimize-descriptions
• devtu-optimize-skills
• devtu-self-evolve
• host-and-share-remote-tool
• setup-boltz-remote-tool
• setup-borzoi-remote-tool
• setup-cell2location-remote-tool
• setup-cellrank-remote-tool
• setup-celltypist-remote-tool
• setup-chrombpnet-remote-tool
• setup-depmap-24q2-remote-tool
• setup-enformer-remote-tool
• setup-esm-remote-tool
• setup-expert-feedback-remote-tool
• setup-harmony-remote-tool
• setup-immune-compass-remote-tool
• setup-ldsc-remote-tool
• setup-liana-remote-tool
• setup-macs3-remote-tool
• setup-milo-remote-tool
• setup-mofa-remote-tool
• setup-monocle3-remote-tool
• setup-paga-remote-tool
• setup-pinnacle-remote-tool
• setup-scanvi-remote-tool
• setup-scrublet-remote-tool
• setup-scvelo-remote-tool
• setup-scvi-remote-tool
• setup-singler-remote-tool
• setup-slingshot-remote-tool
• setup-squidpy-remote-tool
• setup-tangram-remote-tool
• setup-transcriptformer-remote-tool
• setup-uspto-downloader-remote-tool
• tooluniverse-cs-setup

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