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Claude Skills by mims-harvard
github.com/mims-harvard331 skills1 installs379 views
- Tooluniverse Spatial TranscriptomicsSpatial 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 questions, tissue architecture analysis, and SVG identification.Votes: 0GitHub stars: 1,719
- Tooluniverse Statistical ModelingStatistical 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 DM/AE), severity ordinal regression, and per-feature stat workflows.Votes: 0GitHub stars: 1,719
- Tooluniverse Stem Cell OrganoidStem cell, iPSC, and organoid research — pluripotency markers, differentiation protocol pathways, lineage commitment factors, organoid model selection. Use for iPSC characterization, differentiation protocol design via developmental-pathway recapitulation, and organoid-model selection for disease modeling.Votes: 0GitHub stars: 1,719
- Tooluniverse Structural ProteomicsStructural biology plus proteomics integration for drug target validation. Combines PDB experimental structures, AlphaFold predictions, GPCRdb, SAbDab antibody structures, ProteinsPlus binding-site prediction, and BindingDB ligand-affinity data. Use for druggability assessment, binding-site characterization, ligand-pocket analysis, structural-confidence scoring (resolution, pLDDT), and antibody-target interface analysis.Votes: 0GitHub stars: 1,719
- Tooluniverse Structural Variant AnalysisStructural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with ClinGen HI/TS dosage scores, gnomAD frequencies, and ClinVar evidence. Produces 5-tier classification with explicit per-criterion evidence. Use for clinical genomics SV review, dosage-sensitivity assessment, breakpoint analysis, and CNV pathogenicity calls. Gene-dosage-driven reasoning.Votes: 0GitHub stars: 1,719
- Tooluniverse Systems BiologySystems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichment, protein-pathway relationships, network reasoning. Use for pathway analysis on a gene list, multi-source pathway concordance, and systems-level interpretation across databases.Votes: 0GitHub stars: 1,719
- Tooluniverse Target ResearchComprehensive 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 profile reports, target characterization for drug discovery, and 'tell me about target X' queries.Votes: 0GitHub stars: 1,719
- Tooluniverse ToxicologyDrug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, and toxicogenomic associations. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/cardiotoxicity/nephrotoxicity prediction and toxicology reports.Votes: 0GitHub stars: 1,719
- Tooluniverse Vaccine DesignComputational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predicted MHC binding with experimentally validated IEDB epitopes for higher-confidence designs.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant AnalysisVCF 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 (denominator = coding subset only, NOT all variants), and per-sample mutation profiling.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant Functional AnnotationFunctional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies, CADD deleteriousness, ClinGen gene-disease validity, plus FAVOR one-call comprehensive GRCh38 annotation. Use for variant annotation pipelines, missense effect prediction, and protein-level variant interpretation with functional context.Votes: 0GitHub stars: 1,719
- Tooluniverse Variant InterpretationClinical 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), non-coding/regulatory variant effect prediction with sequence deep-learning models (AlphaGenome, Enformer, Borzoi, ChromBPNet, Evo 2), and producing clinical-grade variant reports for return of results or molecular tumor boards. Use this whenever a use...Votes: 0GitHub stars: 1,719
- Tooluniverse Variant Predictor Dms ValidationValidate 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 neutral vs disruptive groups by DMS effect, runs a Mann-Whitney U test on the predictor scores, and sweeps the stratification thresholds for robustness. Use when you need to know whether a predictor's scores track real functional disruption on ...Votes: 0GitHub stars: 1,719
- Tooluniverse Variant To MechanismEnd-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene(s), molecular pathway(s), and phenotypic consequences. Integrates 7+ databases across 3 evidence layers (regulatory, molecular, disease) for a mechanistic model. Use for GWAS-hit-to-mechanism, eQTL-causal-gene tracing, and full causal-chain reports.Votes: 0GitHub stars: 1,719
- Tooluniverse Antigravity PluginInstall, 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), the \"agy plugin install <path>\" flow, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or \"the 1000+ scientific tools\" / \"the harvard tools\") working...Votes: 0GitHub stars: 1,719
- Tooluniverse Nih Funding LandscapeAnalyze NIH grant portfolios and funding history using the OpenNIH FY1985-present corpus, then connect grants to investigators, institutions, publications, clinical trials, patents, targets, or drugs with ToolUniverse. Use for NIH grant discovery, topic or Institute/Center trends, PI and institution profiles, activity-code or mechanism analysis, funding growth and concentration, grant-writing landscape research, SBIR/STTR landscapes, research-policy analysis, expert discovery, funding-to-outp...Votes: 0GitHub stars: 1,719
- Create Tooluniverse SkillCreate high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.Votes: 0GitHub stars: 1,719
- Skill Template[Complete description of what the skill does, which databases it uses, and when to use it. Include specific trigger phrases like "analyze [domain]", "find [data type]", etc. This description is the primary way Claude determines when to use your skill.]Votes: 0GitHub stars: 1,719
- Devtu Auto Discover ApisAutomatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to identify missing tool categories, web searches for APIs, automated tool creation using devtu-create-tool patterns, validation with devtu-fix-tool, and git workflow management. Use when expanding ToolUniverse coverage, adding new API integrations, or systematically discovering scientific resources.Votes: 0GitHub stars: 1,719
- Devtu Benchmark HarnessContinuous improvement system for ToolUniverse tools, skills, and plugin. Run benchmarks, diagnose failures, route fixes to devtu skills, retest. Use after skill optimization, tool additions, or as regression check.Votes: 0GitHub stars: 1,719
- Devtu Code OptimizationCode 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. Triggers: implementing tool fixes, writing new tool classes, reviewing tool code quality, checking schema correctness, looking up API-specific bug fixes.Votes: 0GitHub stars: 1,719
- Devtu Create ToolCreate new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniverse, implement new API integrations, create tool wrappers for scientific databases/services, expand ToolUniverse capabilities, or follow ToolUniverse contribution guidelines. Supports creating tool classes, JSON configurations, validation, error handling, and test examples.Votes: 0GitHub stars: 1,719
- Devtu Docs QualityTOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code, broken links, incorrect counts, and overlapping instructions must be fixed or removed — never left in place. Runs five phases: (D) static method scan, (C) live code execution, (A) automated validation, (B) ToolUniverse audit, (E) less-is-more simplification. Core philosophy: each concept appears exactly once; remove don't add; no emojis; single set...Votes: 0GitHub stars: 1,719
- Devtu Fix ToolFix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUniverse tools fail tests, return errors, have schema validation issues, or when asked to debug or fix tools in the ToolUniverse framework.Votes: 0GitHub stars: 1,719
- Devtu GithubGitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Use when pushing to GitHub, fixing CI failures, or cleaning up before commits.Votes: 0GitHub stars: 1,719
- Devtu Optimize DescriptionsOptimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbreviations, unclear parameters, and missing usage guidance. Use when reviewing tool descriptions, improving API documentation, or when user asks to check if tools are easy to understand.Votes: 0GitHub stars: 1,719
- Devtu Optimize SkillsOptimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, disambiguation-first, evidence grading, quantified completeness, and report-only output. Use when reviewing skills, improving existing skills, or creating new ToolUniverse research skills.Votes: 0GitHub stars: 1,719
- Devtu Self EvolveOrchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills, and push via git. References and dispatches to all other devtu skills. Use when asked to: run the self-improvement loop, do a debug/test round, expand tool coverage, improve tool quality, or evolve ToolUniverse.Votes: 0GitHub stars: 1,719
- Tooluniverse Codex PluginInstall, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS consult this skill for any of those — don't answer from memory, because the exact marketplace name (mims-harvard/ToolUniverse), the "codex plugin marketplace add" then "codex plugin add -m tooluniverse" flow, Codex's startup auto-upgrade behavior, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "...Votes: 0GitHub stars: 1,719
- Tooluniverse Cs SetupInstall 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 ToolUniverse version, refreshing the bundled workflows after an upstream release, or reinstalling on a new machine.Votes: 0GitHub stars: 1,719
- TemplatesBiomedical and scientific research via ToolUniverse's 2500+ tools across 133 structured workflows — drug research, disease research, gene and variant interpretation, cancer genomics, clinical trials, ADMET prediction, pharmacovigilance and adverse events, CRISPR screens, protein and structure analysis, epidemiology, and graded literature reviews. Use for "tell me about drug/gene/disease/variant X", multi-database investigations, cross-validating biomedical claims, ID translation, or any struc...Votes: 0GitHub stars: 1,719