mims-harvard/tooluniverse

1

tooluniverse-adverse-event-detection Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics…

mims-harvard/tooluniverse

351

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tooluniverse-gwas-trait-to-gene Discover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates …

mims-harvard/tooluniverse

349

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tooluniverse-phylogenetics Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighb…

mims-harvard/tooluniverse

349

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tooluniverse-gwas-finemapping Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2…

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348

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tooluniverse-immunotherapy-response-prediction Predict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsa…

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345

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tooluniverse-spatial-omics-analysis Spatial multi-omics interpretation pipeline.

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tooluniverse-immune-repertoire-analysis TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity ma…

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344

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tooluniverse-install-skills Detect and auto-install missing ToolUniverse research skills.

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344

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tooluniverse-multiomic-disease-characterization Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level u…

mims-harvard/tooluniverse

344

10

tooluniverse-gwas-study-explorer Compare GWAS studies, perform meta-analyses across cohorts, and assess signal replication.

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tooluniverse-metabolomics Metabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, M…

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342

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tooluniverse-variant-interpretation Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact anal…

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335

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tooluniverse-polygenic-risk-score Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics.

mims-harvard/tooluniverse

334

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tooluniverse-single-cell Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_gene…

mims-harvard/tooluniverse

316

15

devtu-self-evolve Orchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas,…

mims-harvard/tooluniverse

298

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tooluniverse-custom-tool Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no cod…

mims-harvard/tooluniverse

274

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devtu-code-optimization Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring to…

mims-harvard/tooluniverse

257

18

tooluniverse-organic-chemistry Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic sub…

mims-harvard/tooluniverse

251

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tooluniverse-cancer-genomics-tcga TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, s…

mims-harvard/tooluniverse

250

20

tooluniverse-neuroscience Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric di…

mims-harvard/tooluniverse

246

21

tooluniverse-pharmacogenomics Pharmacogenomics (PGx) research — drug-gene interactions (CPIC, PharmGKB), CPIC dosing guidelines, variant-drug-respo…

mims-harvard/tooluniverse

242

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tooluniverse-drug-regulatory Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug s…

mims-harvard/tooluniverse

241

23

tooluniverse-inorganic-physical-chemistry Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice …

mims-harvard/tooluniverse

235

24

tooluniverse-immunology Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoim…

mims-harvard/tooluniverse

234

25

tooluniverse-metagenomics-analysis Microbiome and metagenomics analysis using MGnify, GTDB taxonomy, ENA sequencing data, and EuropePMC literature.

mims-harvard/tooluniverse

233

26

tooluniverse-ecology-biodiversity Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive spe…

mims-harvard/tooluniverse

232

27

tooluniverse-epidemiological-analysis End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome)…

mims-harvard/tooluniverse

232

28

tooluniverse-dataset-discovery Find and evaluate research datasets for any scientific question.

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229

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tooluniverse-drug-mechanism-research Trace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect →…

mims-harvard/tooluniverse

228

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tooluniverse-toxicology Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FD…

mims-harvard/tooluniverse

228

31

tooluniverse-regulatory-genomics Transcription factor binding, cis-regulatory elements (cCREs), chromatin accessibility, and regulatory annotation usi…

mims-harvard/tooluniverse

227

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tooluniverse-admet-prediction Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates.

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tooluniverse-data-integration-analysis Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse data…

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34

tooluniverse-protein-structure-prediction Protein 3D structure prediction from sequence — ESMFold de novo prediction, AlphaFold database retrieval, experimenta…

mims-harvard/tooluniverse

223

35

tooluniverse-chemical-sourcing Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across…

mims-harvard/tooluniverse

222

36

tooluniverse-data-wrangling Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the so…

mims-harvard/tooluniverse

222

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tooluniverse-clinical-data-integration End-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharma…

mims-harvard/tooluniverse

221

38

tooluniverse-gpcr-structural-pharmacology GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data…

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220

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tooluniverse-small-molecule-discovery Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, e…

mims-harvard/tooluniverse

220

40

tooluniverse-epigenomics-chromatin Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap …

mims-harvard/tooluniverse

219

41

tooluniverse-sequence-analysis Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, o…

mims-harvard/tooluniverse

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tooluniverse-gene-disease-association Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet.

mims-harvard/tooluniverse

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tooluniverse-metabolomics-pathway Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaC…

mims-harvard/tooluniverse

218

44

tooluniverse-pathway-disease-genetics Connect GWAS variants to biological pathways and druggable targets.

mims-harvard/tooluniverse

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tooluniverse-plant-genomics Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, U…

mims-harvard/tooluniverse

218

46

tooluniverse-proteomics-data-retrieval Find and retrieve proteomics datasets from MassIVE and ProteomeXchange.

mims-harvard/tooluniverse

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tooluniverse-structural-proteomics Structural biology plus proteomics integration for drug target validation.

mims-harvard/tooluniverse

218

48

Protein Interaction Network Analysis Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, r…

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217

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tooluniverse-protein-modification-analysis Post-translational modification (PTM) analysis — phosphorylation, ubiquitination, acetylation, glycosylation, methyla…

mims-harvard/tooluniverse

217

50

tooluniverse-adverse-outcome-pathway Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-l…

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