mims-harvard/tooluniverse

7194

tooluniverse-sequence-retrieval Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation.

mims-harvard/tooluniverse

1.6K

2

tooluniverse-literature-deep-research Deep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis.

mims-harvard/tooluniverse

643

3

tooluniverse-image-analysis Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count …

mims-harvard/tooluniverse

637

4

tooluniverse-clinical-guidelines Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, US…

mims-harvard/tooluniverse

466

5

tooluniverse ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run r…

mims-harvard/tooluniverse

458

6

tooluniverse-drug-research Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, advers…

mims-harvard/tooluniverse

452

7

tooluniverse-clinical-trial-design Strategic clinical trial design feasibility assessment.

mims-harvard/tooluniverse

440

8

tooluniverse-drug-drug-interaction Assess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OA…

mims-harvard/tooluniverse

432

9

setup-tooluniverse Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands),…

mims-harvard/tooluniverse

427

10

tooluniverse-disease-research Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEG…

mims-harvard/tooluniverse

419

11

tooluniverse-protein-structure-retrieval Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R…

mims-harvard/tooluniverse

416

12

tooluniverse-systems-biology Systems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interacti…

mims-harvard/tooluniverse

410

13

tooluniverse-network-pharmacology Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi…

mims-harvard/tooluniverse

407

14

tooluniverse-epigenomics Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq…

mims-harvard/tooluniverse

404

15

tooluniverse-pharmacovigilance Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (P…

mims-harvard/tooluniverse

404

16

tooluniverse-precision-oncology Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + inves…

mims-harvard/tooluniverse

403

17

tooluniverse-chemical-compound-retrieval Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry h…

mims-harvard/tooluniverse

400

18

create-tooluniverse-skill Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.

mims-harvard/tooluniverse

394

19

tooluniverse-target-research Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), vari…

mims-harvard/tooluniverse

393

20

tooluniverse-proteomics-analysis Mass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tu…

mims-harvard/tooluniverse

391

21

tooluniverse-spatial-transcriptomics Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq.

mims-harvard/tooluniverse

391

22

tooluniverse-rare-disease-diagnosis Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM)…

mims-harvard/tooluniverse

390

23

tooluniverse-expression-data-retrieval Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality ass…

mims-harvard/tooluniverse

388

24

tooluniverse-rnaseq-deseq2 RNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion est…

mims-harvard/tooluniverse

385

25

tooluniverse-clinical-trial-matching AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular pr…

mims-harvard/tooluniverse

384

26

tooluniverse-drug-repurposing Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies.

mims-harvard/tooluniverse

384

27

tooluniverse-statistical-modeling Statistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, C…

mims-harvard/tooluniverse

384

28

tooluniverse-protein-therapeutic-design AI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation…

mims-harvard/tooluniverse

383

29

tooluniverse-sdk Build AI scientist systems with the ToolUniverse Python SDK for scientific research.

mims-harvard/tooluniverse

382

30

devtu-optimize-skills Optimize ToolUniverse skills for better report quality, evidence handling, and user experience.

mims-harvard/tooluniverse

381

31

tooluniverse-chemical-safety Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experiment…

mims-harvard/tooluniverse

381

32

tooluniverse-multi-omics-integration Multi-omics integration — orchestrate per-layer analysis (transcriptomics, proteomics, epigenomics, genomics, metabol…

mims-harvard/tooluniverse

378

33

devtu-create-tool Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing.

mims-harvard/tooluniverse

377

34

tooluniverse-binder-discovery Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening.

mims-harvard/tooluniverse

376

35

devtu-optimize-descriptions Optimize tool descriptions in ToolUniverse JSON configs for clarity and usability.

mims-harvard/tooluniverse

373

36

tooluniverse-antibody-engineering Therapeutic antibody engineering and optimization, lead-to-clinical-candidate.

mims-harvard/tooluniverse

373

37

tooluniverse-gwas-drug-discovery Transform GWAS signals into drug targets and repurposing opportunities.

mims-harvard/tooluniverse

373

38

devtu-auto-discover-apis Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PR…

mims-harvard/tooluniverse

371

39

tooluniverse-metabolomics-analysis Analyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction…

mims-harvard/tooluniverse

371

40

tooluniverse-gene-enrichment Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathwa…

mims-harvard/tooluniverse

370

41

devtu-fix-tool Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validati…

mims-harvard/tooluniverse

368

42

tooluniverse-drug-target-validation Quantitative drug-target validation pipeline.

mims-harvard/tooluniverse

367

43

tooluniverse-infectious-disease Rapid pathogen characterization and drug repurposing for outbreaks.

mims-harvard/tooluniverse

366

44

tooluniverse-cancer-variant-interpretation Clinical interpretation of somatic cancer mutations for precision oncology.

mims-harvard/tooluniverse

361

45

tooluniverse-precision-medicine-stratification Patient stratification for precision medicine — integrate genomic, clinical, and therapeutic data to split patients i…

mims-harvard/tooluniverse

361

46

tooluniverse-crispr-screen-analysis Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritiza…

mims-harvard/tooluniverse

359

47

tooluniverse-gwas-snp-interpretation Interpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regul…

mims-harvard/tooluniverse

358

48

tooluniverse-structural-variant-analysis Structural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearran…

mims-harvard/tooluniverse

357

49

tooluniverse-variant-analysis VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF f…

mims-harvard/tooluniverse

356

50

devtu-github GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests,…

mims-harvard/tooluniverse

354