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SkillsMP a collecté 339 skills depuis mims-harvard/ToolUniverse. Ouvrez un skill pour examiner sa source et ses détails.
mims-harvard/ToolUniverseAffichage de 40 skills collectés sur 339.
Statistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `ns()`), odds ratios, Cohen's d, F-statistic, p-value computation. Specializes in clinical-trial AE analysis (SDTM…
Langue du texte source : anglais
Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogenicity assessment with cited criteria, structure-based variant impact (AlphaFold/PDB),…
Langue du texte source : anglais
Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (small-angle scattering). Distinguishes physical interactions (binding) from functional associations (co-expression, co-regulation). Use for…
Langue du texte source : anglais
Statistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `ns()`), odds ratios, Cohen's d, F-statistic, p-value computation. Specializes in clinical-trial AE analysis (SDTM…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Install or update ToolUniverse in Claude Science — create the conda env, install the tooluniverse pip package, and (re)build the tooluniverse-research skill by fetching the current workflow library from GitHub. Use for first-time setup, upgrading the…
Langue du texte source : anglais
Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUniverse project. Encodes lessons from 80+ debug rounds. Use alongside devtu-fix-tool and devtu-self-evolve.…
Langue du texte source : anglais
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Covers PRS construction (clumping/thresholding, PRS-CS), validation in independent cohorts, ancestry-aware adjustment, and clinical interpretation…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug…
Langue du texte source : anglais
RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2…
Langue du texte source : anglais
Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression…
Langue du texte source : anglais
VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison. Use for VCF parsing, variant fraction calculations…
Langue du texte source : anglais
Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug…
Langue du texte source : anglais
RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2…
Langue du texte source : anglais
Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression…
Langue du texte source : anglais
VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison. Use for VCF parsing, variant fraction calculations…
Langue du texte source : anglais
Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into…
Langue du texte source : anglais
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…
Langue du texte source : anglais
Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug…
Langue du texte source : anglais
RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2…
Langue du texte source : anglais
VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison. Use for VCF parsing, variant fraction calculations…
Langue du texte source : anglais
Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identification, for ANY target class (GPCR, ion channel, protease, cytokine/growth-factor receptor, enzyme, integrin), not only GPCRs. Use when a…
Langue du texte source : anglais
Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identification, for ANY target class (GPCR, ion channel, protease, cytokine/growth-factor receptor, enzyme, integrin), not only GPCRs. Use when a…
Langue du texte source : anglais
Find the real protein target(s) of a peptide from its sequence — peptide target deorphanization / off-target identification, for ANY target class (GPCR, ion channel, protease, cytokine/growth-factor receptor, enzyme, integrin), not only GPCRs. Use when a…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais