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reflect
Mid-conversation reflection skill that pauses execution and zooms out from detail-mode to honestly reassess direction, assumptions, and bias. Use when the user says 'reflect', 'take a step back', 'step back', 'zoom out', 'are we missing something', 'bigger picture', 'sanity check this', 'are we on track', 'are we overthinking this', 'forest for the trees', …
tooluniverse-meta-analysis
Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean differences, correlations, GWAS betas) with fixed- or random-effects models, quantify heterogeneity (Q, I², τ²), and build a forest plot. Use when you have results from MULTIPLE studies and need a single pooled estimate, or to synthesize evid…
tooluniverse-meta-analysis
Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean differences, correlations, GWAS betas) with fixed- or random-effects models, quantify heterogeneity (Q, I², τ²), and build a forest plot. Use when you have results from MULTIPLE studies and need a single pooled estimate, or to synthesize evid…
tooluniverse-meta-analysis
Meta-analysis / evidence synthesis — pool effect sizes across studies (odds ratios, risk ratios, hazard ratios, mean differences, correlations, GWAS betas) with fixed- or random-effects models, quantify heterogeneity (Q, I², τ²), and build a forest plot. Use when you have results from MULTIPLE studies and need a single pooled estimate, or to synthesize evid…
bio-qsar-modeling
Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic a…
bio-similarity-searching
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when rankin…
bio-clinical-biostatistics-subgroup-analysis
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer…
bio-data-visualization-forest-funnel-plots
Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, tri…
bio-ecological-genomics-landscape-genomics
Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requir…
bio-machine-learning-omics-classifiers
Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the p>>n regime, batch shortcut learning, class imbalance, and probability calibration. Use when building a classifier from expression, methylation, or variant data, choosing an algorithm for high-d…
bio-machine-learning-survival-analysis
Builds and validates predictive time-to-event models on clinical and omics data with penalized Cox, random survival forests, gradient-boosted and deep survival models, and prediction-grade evaluation (Uno's C, time-dependent AUC, integrated Brier, calibration, competing risks). Use when building an individualized risk predictor or prognostic omics signature…
bio-temporal-genomics-temporal-grn
Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives; Random Forests by default, Extra-Trees optional), and dynamic Bayesian networks (bnlearn). Use when the output is a RANKED HYPOTHESIS list for perturbation valida…
data-extractor
Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.
scenario-unreal-world-building
Use when building or fixing an Unreal Engine 5 level or open world: World Partition, OFPA, Data Layers, Level Instances, Packed Level Actors, HLOD, landscape size, heightmap import or clipping, edit layers, terrain material rules, foliage and grass, a PCG forest or rock scatter, runtime GPU grass, Nanite and tessellation choices, modular kits, a river or vi…
data-extractor
Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.
meta-analysis
Perform quantitative meta-analysis with effect size calculation, forest plots, funnel plots, and heterogeneity assessment. Use when: user asks to combine results from multiple studies, calculate pooled effect sizes, assess publication bias, or create forest/funnel plots. NOT for: systematic review protocol (use systematic-review) or single-study statistics …
reflect
Mid-conversation reflection skill that pauses execution and zooms out from detail-mode to honestly reassess direction, assumptions, and bias. Use when the user says 'reflect', 'take a step back', 'step back', 'zoom out', 'are we missing something', 'bigger picture', 'sanity check this', 'are we on track', 'are we overthinking this', 'forest for the trees', …
meta-analysis
Use this Skill to pool effect sizes across studies: fixed/random-effects models, heterogeneity tests (I², Cochran Q), forest plot, funnel plot, Egger test, and subgroup analysis using pymare or manual computation.
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