mims-harvard/tooluniverse
- skills.sh installs
- 28.2K
- skills
- 68
Install
$ npx -y skills add mims-harvard/tooluniverse --agent claude-codeInstalls into .claude/skills of the current project.
Skills
1
tooluniverse-sequence-retrievalmims-harvard/tooluniverseRetrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions1.7Kskills.sh installs
tooluniverse-sequence-retrievalmims-harvard/tooluniverseRetrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions1.7Kskills.sh installs2tooluniverse-literature-deep-researchmims-harvard/tooluniverseDeep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware searches, grad669skills.sh installs
tooluniverse-literature-deep-researchmims-harvard/tooluniverseDeep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware searches, grad669skills.sh installs3tooluniverse-image-analysismims-harvard/tooluniverseMicroscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA656skills.sh installs
tooluniverse-image-analysismims-harvard/tooluniverseMicroscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA656skills.sh installs4tooluniverse-clinical-guidelinesmims-harvard/tooluniverseSearch and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL Eu496skills.sh installs
tooluniverse-clinical-guidelinesmims-harvard/tooluniverseSearch and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL Eu496skills.sh installs5tooluniversemims-harvard/tooluniverseToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<pat485skills.sh installs
tooluniversemims-harvard/tooluniverseToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<pat485skills.sh installs6tooluniverse-drug-researchmims-harvard/tooluniverseComprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and app474skills.sh installs
tooluniverse-drug-researchmims-harvard/tooluniverseComprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and app474skills.sh installs7tooluniverse-clinical-trial-designmims-harvard/tooluniverseStrategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) usin458skills.sh installs
tooluniverse-clinical-trial-designmims-harvard/tooluniverseStrategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) usin458skills.sh installs8tooluniverse-drug-drug-interactionmims-harvard/tooluniverseAssess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic synergy/antago457skills.sh installs
tooluniverse-drug-drug-interactionmims-harvard/tooluniverseAssess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic synergy/antago457skills.sh installs9setup-tooluniversemims-harvard/tooluniverseInstall and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling p448skills.sh installs
setup-tooluniversemims-harvard/tooluniverseInstall and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling p448skills.sh installs10tooluniverse-disease-researchmims-harvard/tooluniverseGenerate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing 439skills.sh installs
tooluniverse-disease-researchmims-harvard/tooluniverseGenerate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing 439skills.sh installs11tooluniverse-systems-biologymims-harvard/tooluniverseSystems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichm436skills.sh installs
tooluniverse-systems-biologymims-harvard/tooluniverseSystems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichm436skills.sh installs12tooluniverse-protein-structure-retrievalmims-harvard/tooluniverseProtein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishe435skills.sh installs
tooluniverse-protein-structure-retrievalmims-harvard/tooluniverseProtein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishe435skills.sh installs13tooluniverse-network-pharmacologymims-harvard/tooluniverseCompound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, 434skills.sh installs
tooluniverse-network-pharmacologymims-harvard/tooluniverseCompound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, 434skills.sh installs14tooluniverse-precision-oncologymims-harvard/tooluniverseCancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms426skills.sh installs
tooluniverse-precision-oncologymims-harvard/tooluniverseCancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms426skills.sh installs15tooluniverse-epigenomicsmims-harvard/tooluniverseGenomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, 425skills.sh installs
tooluniverse-epigenomicsmims-harvard/tooluniverseGenomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, 425skills.sh installs16tooluniverse-pharmacovigilancemims-harvard/tooluniverseDrug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/c424skills.sh installs
tooluniverse-pharmacovigilancemims-harvard/tooluniverseDrug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/c424skills.sh installs17tooluniverse-chemical-compound-retrievalmims-harvard/tooluniverseRetrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names t419skills.sh installs
tooluniverse-chemical-compound-retrievalmims-harvard/tooluniverseRetrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names t419skills.sh installs18create-tooluniverse-skillmims-harvard/tooluniverseCreate high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.412skills.sh installs
create-tooluniverse-skillmims-harvard/tooluniverseCreate high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.412skills.sh installs19tooluniverse-proteomics-analysismims-harvard/tooluniverseMass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tumor vs normal, treatment vs control), PTM i412skills.sh installs
tooluniverse-proteomics-analysismims-harvard/tooluniverseMass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tumor vs normal, treatment vs control), PTM i412skills.sh installs20tooluniverse-target-researchmims-harvard/tooluniverseComprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggabili412skills.sh installs
tooluniverse-target-researchmims-harvard/tooluniverseComprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggabili412skills.sh installs21tooluniverse-spatial-transcriptomicsmims-harvard/tooluniverseSpatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs),411skills.sh installs
tooluniverse-spatial-transcriptomicsmims-harvard/tooluniverseSpatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs),411skills.sh installs22tooluniverse-rare-disease-diagnosismims-harvard/tooluniverseRare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant i410skills.sh installs
tooluniverse-rare-disease-diagnosismims-harvard/tooluniverseRare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant i410skills.sh installs23tooluniverse-rnaseq-deseq2mims-harvard/tooluniverseRNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariat409skills.sh installs
tooluniverse-rnaseq-deseq2mims-harvard/tooluniverseRNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariat409skills.sh installs24tooluniverse-expression-data-retrievalmims-harvard/tooluniverseRetrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray407skills.sh installs
tooluniverse-expression-data-retrievalmims-harvard/tooluniverseRetrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray407skills.sh installs25tooluniverse-statistical-modelingmims-harvard/tooluniverseStatistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `ns()`), odds r407skills.sh installs
tooluniverse-statistical-modelingmims-harvard/tooluniverseStatistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `ns()`), odds r407skills.sh installs26tooluniverse-clinical-trial-matchingmims-harvard/tooluniverseAI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) a406skills.sh installs
tooluniverse-clinical-trial-matchingmims-harvard/tooluniverseAI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) a406skills.sh installs27tooluniverse-drug-repurposingmims-harvard/tooluniverseIdentify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechani400skills.sh installs
tooluniverse-drug-repurposingmims-harvard/tooluniverseIdentify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechani400skills.sh installs28tooluniverse-multi-omics-integrationmims-harvard/tooluniverseMulti-omics integration — orchestrate per-layer analysis (transcriptomics, proteomics, epigenomics, genomics, metabolomics) then perform cross-omics correlation400skills.sh installs
tooluniverse-multi-omics-integrationmims-harvard/tooluniverseMulti-omics integration — orchestrate per-layer analysis (transcriptomics, proteomics, epigenomics, genomics, metabolomics) then perform cross-omics correlation400skills.sh installs29tooluniverse-protein-therapeutic-designmims-harvard/tooluniverseAI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation (pLDDT, pTM, MPNN scores). Use for designi400skills.sh installs
tooluniverse-protein-therapeutic-designmims-harvard/tooluniverseAI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation (pLDDT, pTM, MPNN scores). Use for designi400skills.sh installs30tooluniverse-sdkmims-harvard/tooluniverseBuild AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` fun399skills.sh installs
tooluniverse-sdkmims-harvard/tooluniverseBuild AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` fun399skills.sh installs31tooluniverse-chemical-safetymims-harvard/tooluniverseChemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, an398skills.sh installs
tooluniverse-chemical-safetymims-harvard/tooluniverseChemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, an398skills.sh installs32tooluniverse-binder-discoverymims-harvard/tooluniverseDiscover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining 394skills.sh installs
tooluniverse-binder-discoverymims-harvard/tooluniverseDiscover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining 394skills.sh installs33devtu-optimize-skillsmims-harvard/tooluniverseOptimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, d393skills.sh installs
devtu-optimize-skillsmims-harvard/tooluniverseOptimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, d393skills.sh installs34tooluniverse-metabolomics-analysismims-harvard/tooluniverseAnalyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and pathway inter393skills.sh installs
tooluniverse-metabolomics-analysismims-harvard/tooluniverseAnalyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and pathway inter393skills.sh installs35tooluniverse-antibody-engineeringmims-harvard/tooluniverseTherapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity 391skills.sh installs
tooluniverse-antibody-engineeringmims-harvard/tooluniverseTherapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity 391skills.sh installs36tooluniverse-gene-enrichmentmims-harvard/tooluniverseGene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, O390skills.sh installs
tooluniverse-gene-enrichmentmims-harvard/tooluniverseGene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, O390skills.sh installs37devtu-create-toolmims-harvard/tooluniverseCreate new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, impleme388skills.sh installs
devtu-create-toolmims-harvard/tooluniverseCreate new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, impleme388skills.sh installs38tooluniverse-gwas-drug-discoverymims-harvard/tooluniverseTransform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable 388skills.sh installs
tooluniverse-gwas-drug-discoverymims-harvard/tooluniverseTransform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable 388skills.sh installs39devtu-optimize-descriptionsmims-harvard/tooluniverseOptimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbreviations, unc385skills.sh installs
devtu-optimize-descriptionsmims-harvard/tooluniverseOptimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbreviations, unc385skills.sh installs40tooluniverse-drug-target-validationmims-harvard/tooluniverseQuantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite 384skills.sh installs
tooluniverse-drug-target-validationmims-harvard/tooluniverseQuantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite 384skills.sh installs41tooluniverse-infectious-diseasemims-harvard/tooluniverseRapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases384skills.sh installs
tooluniverse-infectious-diseasemims-harvard/tooluniverseRapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases384skills.sh installs42devtu-auto-discover-apismims-harvard/tooluniverseAutomatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missin383skills.sh installs
devtu-auto-discover-apismims-harvard/tooluniverseAutomatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missin383skills.sh installs43tooluniverse-cancer-variant-interpretationmims-harvard/tooluniverseClinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical 382skills.sh installs
tooluniverse-cancer-variant-interpretationmims-harvard/tooluniverseClinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical 382skills.sh installs44devtu-fix-toolmims-harvard/tooluniverseFix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools f380skills.sh installs
devtu-fix-toolmims-harvard/tooluniverseFix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools f380skills.sh installs45tooluniverse-precision-medicine-stratificationmims-harvard/tooluniversePatient stratification for precision medicine — integrate genomic, clinical, and therapeutic data to split patients into responder/non-responder groups, risk ti377skills.sh installs
tooluniverse-precision-medicine-stratificationmims-harvard/tooluniversePatient stratification for precision medicine — integrate genomic, clinical, and therapeutic data to split patients into responder/non-responder groups, risk ti377skills.sh installs46tooluniverse-gwas-snp-interpretationmims-harvard/tooluniverseInterpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gn376skills.sh installs
tooluniverse-gwas-snp-interpretationmims-harvard/tooluniverseInterpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gn376skills.sh installs47tooluniverse-crispr-screen-analysismims-harvard/tooluniverseAnalyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Us375skills.sh installs
tooluniverse-crispr-screen-analysismims-harvard/tooluniverseAnalyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Us375skills.sh installs48tooluniverse-structural-variant-analysismims-harvard/tooluniverseStructural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with374skills.sh installs
tooluniverse-structural-variant-analysismims-harvard/tooluniverseStructural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with374skills.sh installs49tooluniverse-variant-analysismims-harvard/tooluniverseVCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorizati373skills.sh installs
tooluniverse-variant-analysismims-harvard/tooluniverseVCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorizati373skills.sh installs50tooluniverse-adverse-event-detectionmims-harvard/tooluniverseDetect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative saf371skills.sh installs
tooluniverse-adverse-event-detectionmims-harvard/tooluniverseDetect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative saf371skills.sh installs51devtu-githubmims-harvard/tooluniverseGitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Use when pushin365skills.sh installs
devtu-githubmims-harvard/tooluniverseGitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Use when pushin365skills.sh installs52tooluniverse-gwas-trait-to-genemims-harvard/tooluniverseDiscover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, and distance e365skills.sh installs
tooluniverse-gwas-trait-to-genemims-harvard/tooluniverseDiscover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, and distance e365skills.sh installs53tooluniverse-phylogeneticsmims-harvard/tooluniversePhylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_365skills.sh installs
tooluniverse-phylogeneticsmims-harvard/tooluniversePhylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_365skills.sh installs54tooluniverse-gwas-finemappingmims-harvard/tooluniverseStatistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal variants and t364skills.sh installs
tooluniverse-gwas-finemappingmims-harvard/tooluniverseStatistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal variants and t364skills.sh installs55tooluniverse-spatial-omics-analysismims-harvard/tooluniverseSpatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via dom363skills.sh installs
tooluniverse-spatial-omics-analysismims-harvard/tooluniverseSpatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via dom363skills.sh installs56tooluniverse-immunotherapy-response-predictionmims-harvard/tooluniversePredict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression362skills.sh installs
tooluniverse-immunotherapy-response-predictionmims-harvard/tooluniversePredict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression362skills.sh installs57tooluniverse-immune-repertoire-analysismims-harvard/tooluniverseTCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification361skills.sh installs
tooluniverse-immune-repertoire-analysismims-harvard/tooluniverseTCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification361skills.sh installs58tooluniverse-install-skillsmims-harvard/tooluniverseDetect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any mis361skills.sh installs
tooluniverse-install-skillsmims-harvard/tooluniverseDetect and auto-install missing ToolUniverse research skills. Checks common Claude Code/Cursor/Codex skill directories for the canary file, and installs any mis361skills.sh installs59tooluniverse-multiomic-disease-characterizationmims-harvard/tooluniverseComprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opport360skills.sh installs
tooluniverse-multiomic-disease-characterizationmims-harvard/tooluniverseComprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opport360skills.sh installs60tooluniverse-gwas-study-explorermims-harvard/tooluniverseCompare GWAS studies, perform meta-analyses across cohorts, and assess signal replication. Uses GWAS Catalog metadata, study-level statistics, and cross-cohort 359skills.sh installs
tooluniverse-gwas-study-explorermims-harvard/tooluniverseCompare GWAS studies, perform meta-analyses across cohorts, and assess signal replication. Uses GWAS Catalog metadata, study-level statistics, and cross-cohort 359skills.sh installs61tooluniverse-metabolomicsmims-harvard/tooluniverseMetabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. Use for annota358skills.sh installs
tooluniverse-metabolomicsmims-harvard/tooluniverseMetabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. Use for annota358skills.sh installs62tooluniverse-variant-interpretationmims-harvard/tooluniverseClinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogeni353skills.sh installs
tooluniverse-variant-interpretationmims-harvard/tooluniverseClinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogeni353skills.sh installs63tooluniverse-polygenic-risk-scoremims-harvard/tooluniverseBuild and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Covers PRS construction (clumping/thresholding, PRS-CS), val351skills.sh installs
tooluniverse-polygenic-risk-scoremims-harvard/tooluniverseBuild and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Covers PRS construction (clumping/thresholding, PRS-CS), val351skills.sh installs64tooluniverse-single-cellmims-harvard/tooluniverseSingle-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mitochondrial pe342skills.sh installs
tooluniverse-single-cellmims-harvard/tooluniverseSingle-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mitochondrial pe342skills.sh installs65devtu-self-evolvemims-harvard/tooluniverseOrchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills, and push via 310skills.sh installs
devtu-self-evolvemims-harvard/tooluniverseOrchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills, and push via 310skills.sh installs66tooluniverse-custom-toolmims-harvard/tooluniverseAdd custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL A290skills.sh installs
tooluniverse-custom-toolmims-harvard/tooluniverseAdd custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL A290skills.sh installs67devtu-code-optimizationmims-harvard/tooluniverseCode quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUniverse project.268skills.sh installs
devtu-code-optimizationmims-harvard/tooluniverseCode quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUniverse project.268skills.sh installs68Protein Interaction Network Analysismims-harvard/tooluniverseAnalyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confiden0skills.sh installs
Protein Interaction Network Analysismims-harvard/tooluniverseAnalyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confiden0skills.sh installs