mims-harvard/ToolUniverse - Page 3

setup-scvi-remote-tool

Set up, launch, validate, and troubleshoot the scVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-singler-remote-tool

Set up, launch, validate, and troubleshoot the SingleR ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-slingshot-remote-tool

Set up, launch, validate, and troubleshoot the Slingshot ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-squidpy-remote-tool

Set up, launch, validate, and troubleshoot the Squidpy ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-tangram-remote-tool

Set up, launch, validate, and troubleshoot the Tangram ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-transcriptformer-remote-tool

Set up, launch, validate, and troubleshoot the TranscriptFormer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

setup-uspto-downloader-remote-tool

Set up, launch, validate, and troubleshoot the USPTO downloader ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

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,…

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,…

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,…

tooluniverse-phylogenetics

Phylogenetic analysis — de novo multiple sequence alignment (Clustal Omega/MUSCLE/MAFFT via EBI_msa_align) and neighbour-joining/UPGMA tree building (EBI_build_phylogenetic_tree) from your own sequences, plus tree analysis, treeness, saturation (PhyKIT),…

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…

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…

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.…

tooluniverse-multiomic-disease-characterization

Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opportunities and biomarker candidates by integrating multi-layer molecular data. Use for full-omics…

tooluniverse-target-research

Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggability (DGIdb, ChEMBL approved drugs). 9 parallel research paths with citations. Use for full target…

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…

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.…

tooluniverse-multiomic-disease-characterization

Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opportunities and biomarker candidates by integrating multi-layer molecular data. Use for full-omics…

tooluniverse-target-research

Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggability (DGIdb, ChEMBL approved drugs). 9 parallel research paths with citations. Use for full target…

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.…

tooluniverse-multiomic-disease-characterization

Comprehensive disease characterization across genomics, transcriptomics, proteomics, and pathways for systems-level understanding. Identifies therapeutic opportunities and biomarker candidates by integrating multi-layer molecular data. Use for full-omics…

tooluniverse

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the…

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…

tooluniverse-self-review

Review existing work against the user's actual goal and surface evidence-backed strengths, gaps, risks, and next fixes. Use when asked to eval, evaluate, review, assess, or check current/this/my/our work; decide whether a task is complete; build a…

tooluniverse

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the…

tooluniverse-self-review

Review existing work against the user's actual goal and surface evidence-backed strengths, gaps, risks, and next fixes. Use when asked to eval, evaluate, review, assess, or check current/this/my/our work; decide whether a task is complete; build a…

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,…

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,…

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,…

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…

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…

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),…

tooluniverse-polygenic-risk-score

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…

tooluniverse-precision-oncology

Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms, matching clinical trials, prognosis. Uses CIViC, ClinVar, OpenTargets, ClinicalTrials.gov. Use…

tooluniverse-protein-interactions

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…

tooluniverse-rare-disease-diagnosis

Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis. Use for diagnostic odyssey assistance,…

tooluniverse-statistical-modeling

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…

tooluniverse-polygenic-risk-score

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…

tooluniverse-precision-oncology

Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms, matching clinical trials, prognosis. Uses CIViC, ClinVar, OpenTargets, ClinicalTrials.gov. Use…